From 09c1d4ab75f5cd057ed57bf694217f0e355f785e Mon Sep 17 00:00:00 2001
From: Rand Zoabi <58028465+RZ9082@users.noreply.github.com>
Date: Mon, 11 Nov 2024 11:16:00 +0100
Subject: [PATCH] Cmsearch: added missing args to command (#1328)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* added missing args to command

* bump version

* Bump infernal version, update cmscan test output, and modify cmpress command section

* cmsearch version suffix back to 0

* Lint warnings

* change mapali_cond option order in cmalign

* Lint warning

* Fix cmalign

* data_table set up

* Move DB selector to macros and add cached DB tests

* Re-add unintentionally removed tests

* Fix cmscan

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: paulzierep <paul.zierep@googlemail.com>
---
 tools/rna_tools/infernal/cmalign.xml          | 51 +++++++++----------
 tools/rna_tools/infernal/cmbuild.xml          | 20 ++++----
 tools/rna_tools/infernal/cmpress.xml          | 51 ++++++++-----------
 tools/rna_tools/infernal/cmscan.xml           | 51 ++++++++-----------
 tools/rna_tools/infernal/cmsearch.xml         | 34 +++++--------
 tools/rna_tools/infernal/cmstat.xml           | 34 ++++++-------
 tools/rna_tools/infernal/macros.xml           | 27 ++++++++--
 .../rna_tools/infernal/test-data/infernal.loc | 21 ++++++++
 .../infernal/test-data/test_cmscan.tabular    | 10 ++--
 .../infernal/tool_data_table_conf.xml.sample  |  7 +++
 .../infernal/tool_data_table_conf.xml.test    |  7 +++
 11 files changed, 169 insertions(+), 144 deletions(-)
 create mode 100644 tools/rna_tools/infernal/test-data/infernal.loc
 create mode 100644 tools/rna_tools/infernal/tool_data_table_conf.xml.sample
 create mode 100644 tools/rna_tools/infernal/tool_data_table_conf.xml.test

diff --git a/tools/rna_tools/infernal/cmalign.xml b/tools/rna_tools/infernal/cmalign.xml
index 1f72febe0d..a6ecee7dfb 100644
--- a/tools/rna_tools/infernal/cmalign.xml
+++ b/tools/rna_tools/infernal/cmalign.xml
@@ -3,9 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <expand macro="xrefs"/>
     <command>
 <![CDATA[
 
@@ -33,7 +33,7 @@
                 --mxsize $speed_memory_cont.hmm_banding.mxsize
             #end if
 
-            #if $other_opts.mapali_opt.mapali_cond
+            #if $other_opts.mapali_opt.mapali_cond=="true"
                 --mapali '$other_opts.mapali_opt.mapali'
                 $other_opts.mapali_opt.mapstr
             #end if
@@ -68,26 +68,7 @@
     <inputs>
 
         <param name="seqdb" type="data" format="fasta" label="Sequence database"/>
-
-        <conditional name="cm_opts">
-            <param name="cm_opts_selector" type="select" label="Subject covariance models">
-              <option value="db" selected="True">Locally installed covariance models</option>
-              <option value="histdb">Covariance model from your history</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Covariance models">
-                    <options from_file="infernal.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-            </when>
-            <when value="histdb">
-                <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
-            </when>
-        </conditional>
-
+        <expand macro="DB" />
         <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean"
             label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/>
 
@@ -105,8 +86,11 @@
                 </when>
             </conditional>
             <conditional name="notrunc_opt">
-                <param argument="--notrunc" truevalue="" falsevalue="--notrunc" checked="true" type="boolean"
-                label="Use truncated alignment algorithm" help=""/>
+                <param argument="--notrunc" type="select"
+                label="Use truncated alignment algorithm">
+                    <option value="">Yes</option>
+                    <option value="--notrunc">No</option>
+                </param>
                 <when value=""></when>
                 <when value="--notrunc">
                     <param argument="--sub" type="boolean" truevalue="--sub" falsevalue="" checked="false"
@@ -143,8 +127,11 @@
 
         <section name="other_opts" title="Other options">
             <conditional name="mapali_opt">
-                <param name="mapali_cond" type="boolean" checked="false"
-                    label="Read the aligment file that used to build the CM" help="The alignment from the file is held fixed. This allows you to align sequences to a model with cmalign and view them in the context of an existing trusted multiple alignment."/>
+                <param name="mapali_cond" type="select"
+                    label="Read the aligment file that used to build the CM" help="The alignment from the file is held fixed. This allows you to align sequences to a model with cmalign and view them in the context of an existing trusted multiple alignment.">
+                    <option value="false">No</option>
+                    <option value="true">Yes</option>
+                </param>
                 <when value="true">
                     <param argument="--mapali" type="data" format="fasta"
                         label="The aligment file that used to build the CM" help=""/>
@@ -189,6 +176,18 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <conditional name="cm_opts">
+                <param name="cm_opts_selector" value="db"/>
+                <param name="database" value="cmalign_input2_tRNA5.c.cm"/>
+            </conditional>
+            <param name="seqdb" value="cmalign_input_mrum_tRNAs10.fa"/>
+            <output name="outfile">
+                <assert_contents>
+                    <has_text text="GGAGCUAUAGCUCAAU..GGC"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff --git a/tools/rna_tools/infernal/cmbuild.xml b/tools/rna_tools/infernal/cmbuild.xml
index 4612c9eb5b..26430e01b4 100644
--- a/tools/rna_tools/infernal/cmbuild.xml
+++ b/tools/rna_tools/infernal/cmbuild.xml
@@ -4,9 +4,9 @@
         <import>macros.xml</import>
     </macros>
     <!--parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" merge_outputs="cmfile_outfile"></parallelism-->
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <expand macro="xrefs"/>
     <command>
 <![CDATA[
     cmbuild
@@ -196,19 +196,22 @@
                         <option value="--cyk">align with the CYK algorithm</option>
                     </param>
 
-                    <param name="refine_output" truevalue="" falsevalue="" checked="False" type="boolean"
+                    <param name="refine_output" truevalue="--refine" falsevalue="" checked="False" type="boolean"
                         label="Output the refined alignment file as it is used to build the covariance model" help=""/>
 
                 </when>
             </conditional>
 
-            <param name="is_summery_output" truevalue="" falsevalue="" checked="False" type="boolean"
+            <param name="is_summery_output" truevalue="-o" falsevalue="" checked="False" type="boolean"
                 label="Output a summery file?" help=""/>
 
             <!-- calibrate options -->
             <conditional name="Calibrate">
-                <param name="selector" type="boolean" checked="true" label="Calibrate the covariance model"
-                    help="A CM file must be calibrated with cmcalibrate before it can be used in cmsearch or cmscan. cmcalibrate is very slow. It takes a couple of hours to calibrate a single average sized CM on a single CPU"/>
+                <param name="selector" type="select" label="Calibrate the covariance model"
+                    help="A CM file must be calibrated with cmcalibrate before it can be used in cmsearch or cmscan. cmcalibrate is very slow. It takes a couple of hours to calibrate a single average sized CM on a single CPU">
+                    <option value="true">Yes</option>
+                    <option value="false">No</option>
+                </param>
                 <when value="false"/>
                 <when value="true">
                     <param argument="-L" type="float" value="1.6" min="0.01" max="160" label="Total length of random sequences to search" help="Set random seq length to search in Mb (megabases)"/>
@@ -325,7 +328,7 @@
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="alignment_infile" value="cmbuild_input_tRNA5.sto"/>
             <conditional name="Calibrate">
                 <param name="selector" value="true"/>
@@ -338,7 +341,7 @@
             </output>
         </test>
         <!-- Test emax seq parameter -->
-        <test>
+        <test expect_num_outputs="1">
             <param name="alignment_infile" value="cmbuild_input_tRNA5.sto"/>
             <conditional name="Calibrate">
                 <param name="selector" value="true"/>
@@ -422,8 +425,7 @@ These options control how consensus columns are defined in an alignment.
 
 cmbuild uses an ad hoc sequence weighting algorithm to downweight closely related sequences and upweight distantly related ones. This has the effect of making models less biased by uneven phylogenetic representation. For example, two identical sequences would typically each receive half the weight that one sequence would. These options control which algorithm gets used.
 
-  - *--wgb*: Use the Henikoff position-based sequence weighting scheme [Henikoff
-and Henikoff, J. Mol. Biol. 243:574, 1994].  This is the default.
+  - *--wgb*: Use the Henikoff position-based sequence weighting scheme [Henikoff and Henikoff, J. Mol. Biol. 243:574, 1994].  This is the default.
   - *--wgsc*: Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al, J. Mol. Biol. 235:1067, 1994].
   - *--wnone*: Turn sequence weighting off; e.g. explicitly set all sequence weights to 1.0.
   - *--wgiven*: Use sequence weights as given in annotation in the input alignment file. If no weights were given, assume they are all 1.0. The default is to determine new sequence weights by the Gerstein/Sonnhammer/Chothia algorithm, ignoring any annotated weights.
diff --git a/tools/rna_tools/infernal/cmpress.xml b/tools/rna_tools/infernal/cmpress.xml
index e2525e490a..566d880599 100644
--- a/tools/rna_tools/infernal/cmpress.xml
+++ b/tools/rna_tools/infernal/cmpress.xml
@@ -1,47 +1,27 @@
-<tool id="infernal_cmpress" name="cmpress" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="infernal_cmpress" name="cmpress" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description> Prepare a covariance model database for cmscan</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <expand macro="xrefs"/>
-    <command>
+    <command detect_errors="aggressive">
 <![CDATA[
-    ## CM file from the history or stored as database on disc
+    mkdir -p ./cm_model &&
     #if str($cm_opts.cm_opts_selector) == "db":
-        cmfile_path='$cm_opts.database.fields.path'
+        ln -s '$cm_opts.database.fields.path' ./cm_model/
     #else:
-        ##'$cm_opts.cmfile'
-        cmfile_path='$cmfile'
+        ln -s '$cmfile' ./cm_model/
     #end if
     &&
-    cmpress -F "\$cmfile_path" &&
-    ##cmpress creates four files in the same directory of the cm file
-    cd `dirname "\$cmfile_path"` &&
-    tar -cvf '$outfile' `basename "\$cmfile_path"`.i1*
+    cmpress -F ./cm_model/* &&
+    cd ./cm_model/ &&
+    tar -cvf '$outfile' *.i1f *.i1i *.i1m *.i1p
 ]]>
     </command>
     <inputs>
-        <conditional name="cm_opts">
-            <param name="cm_opts_selector" type="select" label="Subject covariance models &lt;cmdb&gt; ">
-                <option value="db" >Locally installed covariance models</option>
-                <option value="histdb" selected="True">Covariance model from your history</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Covariance models">
-                    <options from_file="infernal.loc">
-                        <column name="value" index="0"/>
-                        <column name="name" index="1"/>
-                        <column name="path" index="2"/>
-                    </options>
-                </param>
-            </when>
-            <when value="histdb">
-                <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
-            </when>
-        </conditional>
-
+        <expand macro="DB" />
     </inputs>
     <outputs>
         <data format="tar" name="outfile" label="cmpress on ${on_string}"/>
@@ -58,7 +38,16 @@
             </assert_stdout>
 
         </test>
+        <test>
+            <conditional name="cm_opts">
+                <param name="cm_opts_selector" value="db"/>
+                <param name="database" value="cmpress_input_minifam.cm"/>
+            </conditional>
+            <assert_stdout>
+                    <has_text text="Working...    done."/>
+            </assert_stdout>
 
+        </test>
     </tests>
     <help>
 <![CDATA[
@@ -86,4 +75,4 @@ For further questions please refere to the Infernal `Userguide <http://eddylab.o
     <expand macro="citations" />
 
 
-</tool>
+</tool>
\ No newline at end of file
diff --git a/tools/rna_tools/infernal/cmscan.xml b/tools/rna_tools/infernal/cmscan.xml
index d90f757cac..b0322c054f 100644
--- a/tools/rna_tools/infernal/cmscan.xml
+++ b/tools/rna_tools/infernal/cmscan.xml
@@ -3,19 +3,21 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
-    <expand macro="xrefs"/>
-    <command>
+    <command detect_errors="aggressive">
 <![CDATA[
     ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
     ## it will be converted to a tab delimited file and piped to Galaxy
     temp_tabular_output=\$(mktemp) &&
 
     #if str($cm_opts.cm_opts_selector) == "histdb":
-        ln -s '$cm_opts.cmfile' cmdb.cm &&
+        ln -s '$cm_opts.cmfile' cmdb.cm
+    #else:
+        ln -s '$cm_opts.database.fields.path' cmdb.cm
     #end if
-
+    &&
     tar xvf '$aux_files' &&
     ln -s `find *.i1f` cmdb.cm.i1f &&
     ln -s `find *.i1i` cmdb.cm.i1i &&
@@ -66,12 +68,7 @@
             #end if
         #end if
         ## CM file from the history or stored as database on disc
-        #if str($cm_opts.cm_opts_selector) == "db":
-            '$cm_opts.database.fields.path'
-        #else:
-            ##'$cm_opts.cmfile'
-            cmdb.cm
-        #end if
+        cmdb.cm
         ## sequence file
         '$seqdb'
         ######### Parse the output file in order to fix a problem reported in https://help.galaxyproject.org/t/messy-infernal-cmscan-output/5984
@@ -92,25 +89,7 @@
     </command>
     <inputs>
         <param name="seqdb" type="data" format="fasta" label="Sequence database &lt;seqfile&gt;"/>
-
-        <conditional name="cm_opts">
-            <param name="cm_opts_selector" type="select" label="Subject covariance models &lt;cmdb&gt; ">
-                <option value="db" >Locally installed covariance models</option>
-                <option value="histdb" selected="True">Covariance model from your history</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Covariance models">
-                    <options from_file="infernal.loc">
-                        <column name="value" index="0"/>
-                        <column name="name" index="1"/>
-                        <column name="path" index="2"/>
-                    </options>
-                </param>
-            </when>
-            <when value="histdb">
-                <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
-            </when>
-        </conditional>
+        <expand macro="DB" />
         <param name="aux_files" type="data" format="tar" label="Auxillury files" help="A tar file contains the four auxillury files suffixed .i1{fimp}. These files are generated after pressing the cm files using cmpress"/>
 
         <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean"
@@ -258,6 +237,20 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <conditional name="cm_opts">
+                <param name="cm_opts_selector" value="db"/>
+                <param name="database" value="minifam.cm" />
+            </conditional>
+            <param name="aux_files" value="minifam.tar" ftype="tar"/>
+            <param name="seqdb" value="metag-example.fa"/>
+            <output name="outfile" file="test_cmscan.tabular" ftype="tabular" lines_diff="8">
+                <assert_contents>
+                    <has_n_lines n="15"/>
+                    <has_text text="AAGA01015927.1"/>
+                </assert_contents>
+            </output>
+        </test>
 
     </tests>
     <help>
diff --git a/tools/rna_tools/infernal/cmsearch.xml b/tools/rna_tools/infernal/cmsearch.xml
index dce8caaf52..fafed5fbf3 100644
--- a/tools/rna_tools/infernal/cmsearch.xml
+++ b/tools/rna_tools/infernal/cmsearch.xml
@@ -4,9 +4,9 @@
         <import>macros.xml</import>
     </macros>
     <!--parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" merge_outputs="outfile,multiple_alignment_output"></parallelism-->
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <expand macro="stdio" />
-    <expand macro="xrefs"/>
     <command>
 <![CDATA[
         ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
@@ -39,6 +39,8 @@
             #if $A:
                 $A '$multiple_alignment_output'
             #end if
+            $noali
+            $verbose
             #if str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incE":
                 --incE $inclusion_thresholds_opts.incE
             #elif str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incT":
@@ -79,25 +81,7 @@
     <inputs>
 
         <param name="seqdb" type="data" format="fasta" label="Sequence database"/>
-
-        <conditional name="cm_opts">
-            <param name="cm_opts_selector" type="select" label="Subject covariance models">
-              <option value="db" selected="True">Locally installed covariance models</option>
-              <option value="histdb">Covariance model from your history</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Covariance models">
-                    <options from_file="infernal.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-            </when>
-            <when value="histdb">
-                <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
-            </when>
-        </conditional>
+        <expand macro="DB" />
 
         <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean"
             label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/>
@@ -241,7 +225,7 @@
 
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="cm_opts">
                 <param name="cm_opts_selector" value="histdb"/>
                 <param name="cmfile" value="cmsearch_input1.cm"/>
@@ -249,6 +233,14 @@
             <param name="seqdb" value="cmsearch_input2.fa"/>
             <output name="outfile" file="cmsearch_result.tabular"/>
         </test>
+        <test expect_num_outputs="1">
+            <conditional name="cm_opts">
+                <param name="cm_opts_selector" value="db"/>
+                <param name="database" value="cmsearch_input1.cm"/>
+            </conditional>
+            <param name="seqdb" value="cmsearch_input2.fa"/>
+            <output name="outfile" file="cmsearch_result.tabular"/>
+        </test>
     </tests>
 
     <help>
diff --git a/tools/rna_tools/infernal/cmstat.xml b/tools/rna_tools/infernal/cmstat.xml
index 115f45a8fc..f946745618 100644
--- a/tools/rna_tools/infernal/cmstat.xml
+++ b/tools/rna_tools/infernal/cmstat.xml
@@ -3,9 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <expand macro="stdio" />
-    <expand macro="xrefs"/>
     <command>
 <![CDATA[
         ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
@@ -25,24 +25,7 @@
 ]]>
     </command>
         <inputs>
-            <conditional name="cm_opts">
-                <param name="cm_opts_selector" type="select" label="Subject covariance models">
-                  <option value="db" selected="True">Locally installed covariance models</option>
-                  <option value="histdb">Covariance model from your history</option>
-                </param>
-                <when value="db">
-                    <param name="database" type="select" label="Covariance models">
-                        <options from_file="infernal.loc">
-                          <column name="value" index="0"/>
-                          <column name="name" index="1"/>
-                          <column name="path" index="2"/>
-                        </options>
-                    </param>
-                </when>
-                <when value="histdb">
-                    <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
-                </when>
-            </conditional>
+            <expand macro="DB" />
         </inputs>
     <outputs>
         <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
@@ -61,6 +44,19 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <conditional name="cm_opts">
+                <param name="cm_opts_selector" value="db"/>
+                <param name="database" value="cmstat_input.cm"/>
+            </conditional>
+            <output name="outfile" >
+                <assert_contents>
+                    <has_text text="idx"/>
+                    <has_text text="accession"/>
+                    <has_text text="nseq"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff --git a/tools/rna_tools/infernal/macros.xml b/tools/rna_tools/infernal/macros.xml
index 48b0ac5f9e..3d05f43543 100644
--- a/tools/rna_tools/infernal/macros.xml
+++ b/tools/rna_tools/infernal/macros.xml
@@ -1,18 +1,37 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package">infernal</requirement>
-            <requirement type="package" version="1.1.4">infernal</requirement>
-            <requirement type="package" version="8.32">coreutils</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">infernal</requirement>
+            <requirement type="package" version="9.5">coreutils</requirement>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">1.1.4</token>
+    <token name="@TOOL_VERSION@">1.1.5</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="xrefs">
         <xrefs>
             <xref type="bio.tools">infernal</xref>
         </xrefs>
     </xml>
+    <xml name="DB">
+        <conditional name="cm_opts">
+            <param name="cm_opts_selector" type="select" label="Subject covariance models">
+              <option value="db" selected="True">Locally installed covariance models</option>
+              <option value="histdb">Covariance model from your history</option>
+            </param>
+            <when value="db">
+                <param name="database" type="select" label="Covariance models">
+                    <options from_data_table="infernal">
+                      <column name="value" index="0"/>
+                      <column name="name" index="1"/>
+                      <column name="path" index="2"/>
+                    </options>
+                </param>
+            </when>
+            <when value="histdb">
+                <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
+            </when>
+        </conditional>
+    </xml>
     <xml name="stdio">
         <stdio>
             <exit_code range="1:" />
diff --git a/tools/rna_tools/infernal/test-data/infernal.loc b/tools/rna_tools/infernal/test-data/infernal.loc
new file mode 100644
index 0000000000..ca529f3a7a
--- /dev/null
+++ b/tools/rna_tools/infernal/test-data/infernal.loc
@@ -0,0 +1,21 @@
+#This is a sample file distributed with Galaxy that is used to define a
+#list of infernal covariance models, using three columns tab separated
+#(longer whitespace are TAB characters):
+#
+#The entries are as follows:
+#
+#<unique_id>	<covariance model name>	<path>
+#
+#Your infernal.loc file should include an entry per line for each "base name" 
+#you have stored.  For example:
+#
+#rfam01	RFAM 4.2 08 Aug 2013	/data/0/galaxy_data/infernal/08_08_2013/rfam.cm
+#
+#...etc...
+#
+
+cmstat_input.cm	Test case: cmstat_input	${__HERE__}/cmstat_input.cm
+cmsearch_input1.cm	Test case: cmsearch_input1	${__HERE__}/cmsearch_input1.cm
+minifam.cm	Test case: minifam.cm	${__HERE__}/minifam.cm
+cmpress_input_minifam.cm	Test case: cmpress_input_minifam.cm	${__HERE__}/cmpress_input_minifam.cm
+cmalign_input2_tRNA5.c.cm	Test case: cmalign_input2_tRNA5.c.cm	${__HERE__}/cmalign_input2_tRNA5.c.cm
diff --git a/tools/rna_tools/infernal/test-data/test_cmscan.tabular b/tools/rna_tools/infernal/test-data/test_cmscan.tabular
index cfd749f2b0..c84463a9d4 100644
--- a/tools/rna_tools/infernal/test-data/test_cmscan.tabular
+++ b/tools/rna_tools/infernal/test-data/test_cmscan.tabular
@@ -5,11 +5,11 @@ tRNA5	-	AAGA01015927.1	-	cm	1	72	314	386	+	no	1	0.59	0.0	53.5	6e-16	!
 Cobalamin	RF00174	AAFY01022046.1	-	cm	32	191	934	832	-	5'	2	0.48	0.0	30.0	6.1e-09	!	                 Cobalamin riboswitch
 #																	                
 #	Program:	cmscan															                
-#	Version:	1.1.4	(Dec	2020)													                
+#	Version:	1.1.5	(Sep	2023)													                
 #	Pipeline	mode:	SCAN														                
-#	Query	file:	/tmp/tmp6jwp47cs/files/a/6/f/dataset_a6fe922b-72aa-4753-b4dd-cd3c716a4ae5.dat														                
+#	Query	file:	/tmp/tmpst0r7qh9/files/7/3/7/dataset_7373cb0d-0d12-49b5-96e0-e1aabaa6db38.dat														                
 #	Target	file:	cmdb.cm														                
-#	Option	settings:	cmscan	-o	/dev/null	--tblout	$temp_tabular_output	--default	--cpu	1	cmdb.cm	/tmp/tmp6jwp47cs/files/a/6/f/dataset_a6fe922b-72aa-4753-b4dd-cd3c716a4ae5.dat					                
-#	Current	dir:	/tmp/tmp6jwp47cs/job_working_directory/000/13/working														                
-#	Date:	Thu	Sep	23	15:21:39	2021											                
+#	Option	settings:	cmscan	-o	/dev/null	--tblout	$temp_tabular_output	--default	--cpu	1	cmdb.cm	/tmp/tmpst0r7qh9/files/7/3/7/dataset_7373cb0d-0d12-49b5-96e0-e1aabaa6db38.dat					                
+#	Current	dir:	/tmp/tmpst0r7qh9/job_working_directory/000/4/working														                
+#	Date:	Thu	Oct	17	11:28:32	2024											                
 #	[ok]																                
diff --git a/tools/rna_tools/infernal/tool_data_table_conf.xml.sample b/tools/rna_tools/infernal/tool_data_table_conf.xml.sample
new file mode 100644
index 0000000000..6f694f25cf
--- /dev/null
+++ b/tools/rna_tools/infernal/tool_data_table_conf.xml.sample
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of infernal database files -->
+    <table name="infernal" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/infernal.loc" />
+    </table>
+</tables>
\ No newline at end of file
diff --git a/tools/rna_tools/infernal/tool_data_table_conf.xml.test b/tools/rna_tools/infernal/tool_data_table_conf.xml.test
new file mode 100644
index 0000000000..5d68755faa
--- /dev/null
+++ b/tools/rna_tools/infernal/tool_data_table_conf.xml.test
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of infernal database files -->
+    <table name="infernal" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/infernal.loc" />
+    </table>
+</tables>
\ No newline at end of file