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add new -y parameter, bump version, adopt tests, WIP
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@bgruening
bgruening committed Dec 2, 2024
1 parent f8d8a93 commit db3e992
Showing 1 changed file with 47 additions and 17 deletions.
64 changes: 47 additions & 17 deletions tools/diff/diff.xml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="23.0">
<description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>
<macros>
<token name="@TOOL_VERSION@">3.7</token>
<token name="@TOOL_VERSION@">3.10</token>
<token name="@GALAXY_VERSION@">0</token>
</macros>
<requirements>
Expand All @@ -13,8 +13,15 @@
<regex match="diff: memory exhausted" source="stdout" level="fatal_oom" description="Out of memory error occurred"/>
</stdio>
<command><![CDATA[
diff -u '$input1' '$input2' > '$diff_file';
#if $generate_report:
diff
#if $report_format.report_format_select in ['txt_lines', 'html']:
## the -u option is needed to convert the output later to HTML
-u
#else if $report_format.report_format_select == 'txt_columns':
-y
#end if
'$input1' '$input2' > '$diff_file' &&
#if $report_format.report_format_select == 'html':
sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'
-e 's/@@outputformat@@/'$output_format'/g'
-e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
Expand All @@ -25,11 +32,21 @@
<inputs>
<param name="input1" type="data" format="txt" label="First input file"/>
<param name="input2" type="data" format="txt" label="Second input file"/>
<param name="generate_report" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate HTML report" help="Generates an HTML report to visualize the differences"/>
<param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side.">
<option value="side-by-side">Side by side</option>
<option value="line-by-line">Line by line</option>
</param>
<conditional name="report_format">
<param name="report_format_select" type="select" label="Choose a report format">
<option value="txt_lines">Text file, line-by-line (-u)</option>
<option value="txt_columns">Text file, side-by-side (-y)</option>
<option value="html">Generates an HTML report to visualize the differences</option>
</param>
<when value="txt_lines"/>
<when value="txt_columns"/>
<when value="html">
<param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side.">
<option value="side-by-side">Side by side</option>
<option value="line-by-line">Line by line</option>
</param>
</when>
</conditional>
</inputs>
<outputs>
<data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output"/>
Expand All @@ -41,7 +58,9 @@
<test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
<param name="input1" value="file1.txt"/>
<param name="input2" value="file1.txt"/>
<param name="generate_report" value="false"/>
<conditional name="report_format">
<param name="report_format_select" value="txt_lines"/>
</conditional>
<output name="diff_file">
<assert_contents>
<has_n_lines n="0"/>
Expand All @@ -51,7 +70,9 @@
<test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
<param name="input1" value="file1.txt"/>
<param name="input2" value="file2.txt"/>
<param name="generate_report" value="false"/>
<conditional name="report_format">
<param name="report_format_select" value="txt_lines"/>
</conditional>
<output name="diff_file">
<assert_contents>
<has_n_lines n="5"/>
Expand All @@ -63,7 +84,9 @@
<test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
<param name="input1" value="file1.txt"/>
<param name="input2" value="file2.txt"/>
<param name="generate_report" value="true"/>
<conditional name="report_format">
<param name="report_format_select" value="html"/>
</conditional>
<output name="html_file">
<assert_contents>
<has_text text="!DOCTYPE html"/>
Expand All @@ -73,8 +96,10 @@
<test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
<param name="input1" value="file1.txt"/>
<param name="input2" value="file2.txt"/>
<param name="generate_report" value="true"/>
<param name="output_format" value="side-by-side"/>
<conditional name="report_format">
<param name="report_format_select" value="html"/>
<param name="output_format" value="side-by-side"/>
</conditional>
<output name="html_file">
<assert_contents>
<has_text text="!DOCTYPE html"/>
Expand All @@ -85,8 +110,10 @@
<test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
<param name="input1" value="file1.txt"/>
<param name="input2" value="file2.txt"/>
<param name="generate_report" value="true"/>
<param name="output_format" value="line-by-line"/>
<conditional name="report_format">
<param name="report_format_select" value="html"/>
<param name="output_format" value="line-by-line"/>
</conditional>
<output name="html_file">
<assert_contents>
<has_text text="!DOCTYPE html"/>
Expand All @@ -97,7 +124,10 @@
<test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
<param name="input1" value="file 3.txt"/>
<param name="input2" value="file 3.txt"/>
<param name="generate_report" value="true"/>
<conditional name="report_format">
<param name="report_format_select" value="html"/>
<param name="output_format" value="side-by-side"/>
</conditional>
<output name="diff_file">
<assert_contents>
<has_n_lines n="0"/>
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