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Diff add -y parameter #1555

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merged 11 commits into from
Dec 9, 2024
Merged

Diff add -y parameter #1555

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db3e992
add new -y parameter, bump version, adopt tests, WIP
bgruening Dec 2, 2024
deb7f1c
Update diff.xml
bgruening Dec 2, 2024
66f1622
Update diff.xml
bgruening Dec 2, 2024
667a7ac
add unified option with integer
bgruening Dec 2, 2024
c4f6fed
fix another missing template
bgruening Dec 2, 2024
6cc4955
adjust command and input/output sections and add tests
RZ9082 Dec 4, 2024
9ce769e
increment version suffix
RZ9082 Dec 4, 2024
174ef20
re-add profile
RZ9082 Dec 4, 2024
a780555
handle diff exit-code 1
RZ9082 Dec 9, 2024
fd72412
add a comment
RZ9082 Dec 9, 2024
3c61e1c
typo
RZ9082 Dec 9, 2024
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80 changes: 57 additions & 23 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 @@ -13,10 +13,18 @@
<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 == 'txt_lines' or $report_format.report_format_select == 'html'
## the -u option is needed to convert the output later to HTML
--unified=$report_format.unified
#else if $report_format.report_format_select == 'txt_columns'
-y
#end if
## If the compared input files differ the diff command returns exit-code 1
'$input1' '$input2' > '$diff_file' || [ \$? -eq 1 ];
#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 's/@@outputformat@@/'$report_format.output_format'/g'
-e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
'$__tool_directory__/template.html' > '$html_file'
#end if
Expand All @@ -25,33 +33,50 @@
<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">
<param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>
</when>
<when value="txt_columns"/>
<when value="html">
<param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>
<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 ${on_string}: Raw Output"/>
<data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Html Report">
<filter>generate_report is True</filter>
<filter>report_format['report_format_select'] == 'html'</filter>
</data>
</outputs>
<tests>
<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"/>
</assert_contents>
</output>
</test>
<test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
<test expect_exit_code="0" 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 +88,9 @@
<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 +100,10 @@
<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 +114,10 @@
<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 @@ -95,9 +126,12 @@
</output>
</test>
<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"/>
<param name="input1" value="file3.txt"/>
<param name="input2" value="file3.txt"/>
<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"/>
Expand Down Expand Up @@ -169,4 +203,4 @@ An **optional** *HTML report* with a friendlier visual representation of the dif
}
</citation>
</citations>
</tool>
</tool>
0 tools/diff/test-data/file 3.txt → tools/diff/test-data/file3.txt
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2 changes: 2 additions & 0 deletions tools/diff/test-data/output_test4.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
a a
> b
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