| Previous changeset 3:be06c14e543d (2018-03-23) Next changeset 5:7fbd66f985b7 (2018-04-10) |
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Commit message:
planemo upload commit 34edf9c3db61650a03d5a0d548b9697a94ecde34-dirty |
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modified:
README.rst reactome_analysis.py reactome_analysis.xml template.html test-data/ID_Converter_FKW_Lacombe_et_al_2017_OK.txt test-data/Reactome_Analysis_Tools.html test-data/Reactome_Analysis_Tools_invalid_ID.txt |
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| diff -r be06c14e543d -r 878128362e33 reactome_analysis.py --- a/reactome_analysis.py Fri Mar 23 10:48:36 2018 -0400 +++ b/reactome_analysis.py Tue Apr 03 08:24:45 2018 -0400 |
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| @@ -23,8 +23,8 @@ """ Check if an variable is numeric """ - float_format = re.compile("^[\-]?[1-9][0-9]*\.?[0-9]+$") - int_format = re.compile("^[\-]?[1-9][0-9]*$") + float_format = re.compile(r"^[-]?[1-9][0-9]*.?[0-9]+$") + int_format = re.compile(r"^[-]?[1-9][0-9]*$") test = "" if format == "int": test = re.match(int_format, n) @@ -81,9 +81,11 @@ template.close() output.close() - trash_out = open(trash_file, "w") - trash_out.write("\n".join(trash)) - trash_out.close() + if trash: + print(trash) + trash_out = open(trash_file, "w") + trash_out.write("\n".join(trash)) + trash_out.close() def options(): parser = argparse.ArgumentParser() |
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| diff -r be06c14e543d -r 878128362e33 reactome_analysis.xml --- a/reactome_analysis.xml Fri Mar 23 10:48:36 2018 -0400 +++ b/reactome_analysis.xml Tue Apr 03 08:24:45 2018 -0400 |
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| @@ -21,7 +21,16 @@ <option value="file" selected="true">Input file containing your identifiers</option> </param> <when value="text" > - <param name="list" type="text" label="Enter list of identifiers" /> + <param name="list" type="text" label="Enter list of identifiers" help="IDs must be separated by space into the form field, for example: P31946 P62258"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> </when> <when value="file" > <param name="file" type="data" format="txt, tabular" label="Input file containing your identifiers" help="Input file is a tab-delimited file containing different information of proteins, such as an output of MaxQuant software" /> @@ -33,7 +42,9 @@ </inputs> <outputs> <data name="output" format="html" label="" /> - <data name="trash" format="tabular" label="Invalid identifiers" /> + <data name="trash" format="tabular" hidden="true" label="Invalid id not send to reactome"> + <discover_datasets pattern="(Reactome_Analysis_Tools_invalid_ID).txt" ext="txt" visible="false" assign_primary_output="false"/> + </data> </outputs> <tests> <test> @@ -44,7 +55,7 @@ <param name="ncol" value="c1" /> </conditional> <output name="output" file="Reactome_Analysis_Tools.html" ftype="html" /> - <output name="trash" file="Reactome_Analysis_Tools_invalid_ID.txt" ftype="tab" /> + <!-- <output name="trash" file="Reactome_Analysis_Tools_invalid_ID.txt" ftype="tab" hidden="true" /> --> </test> </tests> <help><![CDATA[ |