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add new -y parameter, bump version, adopt tests, WIP #1554

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add new -y parameter, bump version, adopt tests, WIP #1554

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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
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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'
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Should the last && be placed inside the condition?

I think that might be the issue here: https://github.com/bgruening/galaxytools/actions/runs/12117476870?pr=1554

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Yes, this was really not tested. Just did it really quick to get it started. I hope the -y option can help Danielas use-case

-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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