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planemo upload commit b5afbd13a9ecfc706597cd93681eb5c1be3145e9-dirty |
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README revigoWrapper.xml test-data/test.tab test-data/test1.out test-data/test2.out |
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| diff -r 000000000000 -r ebc00346c9eb README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Sep 25 18:21:03 2017 -0400 |
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| @@ -0,0 +1,1 @@ +tool to prepare data for REVIGO |
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| diff -r 000000000000 -r ebc00346c9eb revigoWrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/revigoWrapper.xml Mon Sep 25 18:21:03 2017 -0400 |
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| @@ -0,0 +1,74 @@ +<tool id="revigo-data-prep" name="Prepare Data for REVIGO" version="0.1"> + <description>Cut columns from tabular data and define as REVIGO datatype.</description> + <command> + #if ($include_numeric.include_numeric_column == "yes"): + awk + '{ print \$goTermsCol"\t"\$numberCol}' + goTermsCol=$goTermsCol + numberCol=$include_numeric.numberCol + $input > $out_file1 + #else + awk '{ print \$goTermsCol}' + goTermsCol=$goTermsCol + $input > $out_file1 + #end if + </command> + <inputs> + <param format="tabular" name="input" type="data" label="Input Dataset" /> + <param name="goTermsCol" + type="data_column" + data_ref="input" + value="1" + accept_default="true" + label="Select Column of GO Terms" /> + <conditional name="include_numeric"> + <param name="include_numeric_column" type="select" label="Include measures of enrichment?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="numberCol" + type="data_column" + data_ref="input" + value="2" + accept_default="true" + label="Select Column of p-values, etc." /> + </when> + </conditional> + </inputs> + <outputs> + <data format="revigo" + name="out_file1" + metadata_source="input" + label="Prepare ${on_string} for REVIGO"/> + </outputs> + <tests> + <test> + <param name="input" value="test.tab" ftype="tabular" /> + <param name="goTermsCol" value="1"/> + <param name="include_numeric_column" value="yes"/> + <param name="numberCol" value="3"/> + <output name="out_file1" file="test1.out" ftype="revigo"/> + </test> + <test> + <param name="input" value="test.tab" ftype="tabular" /> + <param name="goTermsCol" value="1"/> + <param name="include_numeric_column" value="no"/> + <output name="out_file1" file="test2.out" ftype="revigo"/> + </test> + </tests> + <help> +Prepare data for REVIGO + </help> + <citations> + <citation type="bibtex"> + @misc{REVIGOtool, + author = {Caleb Easterly}, + date = {22 Sept 2017}, + title = {REVIGO Data Prep Tool} + } + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r ebc00346c9eb test-data/test.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.tab Mon Sep 25 18:21:03 2017 -0400 |
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| @@ -0,0 +1,2 @@ +GO:123 blah 0.001 otherdata +GO:456 blah 0.002 other |
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| diff -r 000000000000 -r ebc00346c9eb test-data/test1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.out Mon Sep 25 18:21:03 2017 -0400 |
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| @@ -0,0 +1,2 @@ +GO:123 0.001 +GO:456 0.002 |
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| diff -r 000000000000 -r ebc00346c9eb test-data/test2.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.out Mon Sep 25 18:21:03 2017 -0400 |
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| @@ -0,0 +1,2 @@ +GO:123 +GO:456 |