| Previous changeset 3:156d0908e232 (2021-03-12) Next changeset 5:be2d899bf34a (2025-04-09) |
|
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 1a6c4a793ef68a43de93316523c1cd9196d80b73 |
|
modified:
diff.xml |
|
added:
test-data/file3.txt test-data/output_test4.txt |
|
removed:
test-data/file 3.txt |
| b |
| diff -r 156d0908e232 -r 10ef1bf99074 diff.xml --- a/diff.xml Fri Mar 12 16:22:44 2021 +0000 +++ b/diff.xml Mon Dec 09 14:36:40 2024 +0000 |
| [ |
| b'@@ -1,7 +1,7 @@\n-<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">\n+<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="23.0">\n <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>\n <macros>\n- <token name="@TOOL_VERSION@">3.7</token>\n+ <token name="@TOOL_VERSION@">3.10</token>\n <token name="@GALAXY_VERSION@">0</token>\n </macros>\n <requirements>\n@@ -13,10 +13,18 @@\n <regex match="diff: memory exhausted" source="stdout" level="fatal_oom" description="Out of memory error occurred"/>\n </stdio>\n <command><![CDATA[\n- diff -u \'$input1\' \'$input2\' > \'$diff_file\';\n- #if $generate_report:\n+ diff\n+ #if $report_format.report_format_select == \'txt_lines\' or $report_format.report_format_select == \'html\'\n+ ## the -u option is needed to convert the output later to HTML\n+ --unified=$report_format.unified\n+ #else if $report_format.report_format_select == \'txt_columns\'\n+ -y\n+ #end if\n+ ## If the compared input files differ the diff command returns exit-code 1\n+ \'$input1\' \'$input2\' > \'$diff_file\' || [ \\$? -eq 1 ];\n+ #if $report_format.report_format_select == \'html\'\n sed -e \'s/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g\'\n- -e \'s/@@outputformat@@/\'$output_format\'/g\'\n+ -e \'s/@@outputformat@@/\'$report_format.output_format\'/g\'\n -e \'/@@diffoutput@@/{r\'$diff_file\'\' -e \';d}\'\n \'$__tool_directory__/template.html\' > \'$html_file\'\n #end if\n@@ -25,33 +33,50 @@\n <inputs>\n <param name="input1" type="data" format="txt" label="First input file"/>\n <param name="input2" type="data" format="txt" label="Second input file"/>\n- <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"/>\n- <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.">\n- <option value="side-by-side">Side by side</option>\n- <option value="line-by-line">Line by line</option>\n- </param>\n+ <conditional name="report_format">\n+ <param name="report_format_select" type="select" label="Choose a report format">\n+ <option value="txt_lines">Text file, line-by-line (-u)</option>\n+ <option value="txt_columns">Text file, side-by-side (-y)</option>\n+ <option value="html">Generates an HTML report to visualize the differences</option>\n+ </param>\n+ <when value="txt_lines">\n+ <param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>\n+ </when>\n+ <when value="txt_columns"/>\n+ <when value="html">\n+ <param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>\n+ <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.">\n+ <option value="side-by-side">Side by side</option>\n+ <option value="line-by-line">Line by line</option>\n+ </param>\n+ </when>\n+ </conditional>\n </inputs>\n <outputs>\n <data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output"/>\n <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on'..b'= \'html\'</filter>\n </data>\n </outputs>\n <tests>\n <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">\n <param name="input1" value="file1.txt"/>\n <param name="input2" value="file1.txt"/>\n- <param name="generate_report" value="false"/>\n+ <conditional name="report_format">\n+ <param name="report_format_select" value="txt_lines"/>\n+ </conditional>\n <output name="diff_file">\n <assert_contents>\n <has_n_lines n="0"/>\n </assert_contents>\n </output>\n </test>\n- <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">\n+ <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">\n <param name="input1" value="file1.txt"/>\n <param name="input2" value="file2.txt"/>\n- <param name="generate_report" value="false"/>\n+ <conditional name="report_format">\n+ <param name="report_format_select" value="txt_lines"/>\n+ </conditional>\n <output name="diff_file">\n <assert_contents>\n <has_n_lines n="5"/>\n@@ -63,7 +88,9 @@\n <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">\n <param name="input1" value="file1.txt"/>\n <param name="input2" value="file2.txt"/>\n- <param name="generate_report" value="true"/>\n+ <conditional name="report_format">\n+ <param name="report_format_select" value="html"/>\n+ </conditional>\n <output name="html_file">\n <assert_contents>\n <has_text text="!DOCTYPE html"/>\n@@ -73,8 +100,10 @@\n <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">\n <param name="input1" value="file1.txt"/>\n <param name="input2" value="file2.txt"/>\n- <param name="generate_report" value="true"/>\n- <param name="output_format" value="side-by-side"/>\n+ <conditional name="report_format">\n+ <param name="report_format_select" value="html"/>\n+ <param name="output_format" value="side-by-side"/>\n+ </conditional>\n <output name="html_file">\n <assert_contents>\n <has_text text="!DOCTYPE html"/>\n@@ -85,8 +114,10 @@\n <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">\n <param name="input1" value="file1.txt"/>\n <param name="input2" value="file2.txt"/>\n- <param name="generate_report" value="true"/>\n- <param name="output_format" value="line-by-line"/>\n+ <conditional name="report_format">\n+ <param name="report_format_select" value="html"/>\n+ <param name="output_format" value="line-by-line"/>\n+ </conditional>\n <output name="html_file">\n <assert_contents>\n <has_text text="!DOCTYPE html"/>\n@@ -95,9 +126,12 @@\n </output>\n </test>\n <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">\n- <param name="input1" value="file 3.txt"/>\n- <param name="input2" value="file 3.txt"/>\n- <param name="generate_report" value="true"/>\n+ <param name="input1" value="file3.txt"/>\n+ <param name="input2" value="file3.txt"/>\n+ <conditional name="report_format">\n+ <param name="report_format_select" value="html"/>\n+ <param name="output_format" value="side-by-side"/>\n+ </conditional>\n <output name="diff_file">\n <assert_contents>\n <has_n_lines n="0"/>\n@@ -169,4 +203,4 @@\n }\n </citation>\n </citations>\n-</tool>\n+</tool>\n\\ No newline at end of file\n' |
| b |
| diff -r 156d0908e232 -r 10ef1bf99074 test-data/file 3.txt --- a/test-data/file 3.txt Fri Mar 12 16:22:44 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -c |
| b |
| diff -r 156d0908e232 -r 10ef1bf99074 test-data/file3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/file3.txt Mon Dec 09 14:36:40 2024 +0000 |
| b |
| @@ -0,0 +1,1 @@ +c |
| b |
| diff -r 156d0908e232 -r 10ef1bf99074 test-data/output_test4.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_test4.txt Mon Dec 09 14:36:40 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +a a + > b |