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Merge pull request #8 from workflow4metabolomics/section
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,2 @@ | ||
| tool_test_output.html | ||
| tool_test_output.json |
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@@ -27,32 +27,30 @@ | |
| <!-- raw file load for planemo test --> | ||
| <token name="@COMMAND_FILE_LOAD_NEUTRAL@"> | ||
| #if $file_load_section_selected.file_load_conditional.file_load_select == "yes": | ||
| #if $file_load_section_selected.file_load_conditional.inputs.input == "zip_file": | ||
| zipfile$polarity '$file_load_section_selected.file_load_conditional.inputs.zip_file' | ||
| #if $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("netcdf"): | ||
| #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section_selected.file_load_conditional.input ] ) | ||
| #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section_selected.file_load_conditional.input ] ) | ||
| singlefile_galaxyPath$polarity '$singlefile_galaxyPath' singlefile_sampleName$polarity '$singlefile_sampleName' | ||
| #else | ||
| #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section_selected.file_load_conditional.inputs.single_file ] ) | ||
| #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section_selected.file_load_conditional.inputs.single_file ] ) | ||
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| singlefile_galaxyPath$polarity '$singlefile_galaxyPath' | ||
| singlefile_sampleName$polarity '$singlefile_sampleName' | ||
| zipfile$polarity '$file_load_section_selected.file_load_conditional.input' | ||
| #end if | ||
| #end if | ||
| </token> | ||
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| <token name="@COMMAND_FILE_LOAD_ONE@"> | ||
| #set file_load_section_selected = $file_load_section | ||
| #set file_load_section_selected = $acquisition_options.file_load_section | ||
| #set polarity="" | ||
| @COMMAND_FILE_LOAD_NEUTRAL@ | ||
| </token> | ||
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| <token name="@COMMAND_FILE_LOAD_POSITIVE@"> | ||
| #set file_load_section_selected = $file_load_sectionPositive | ||
| #set file_load_section_selected = $acquisition_options.file_load_sectionPositive | ||
| #set polarity="Positive" | ||
| @COMMAND_FILE_LOAD_NEUTRAL@ | ||
| </token> | ||
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| <token name="@COMMAND_FILE_LOAD_NEGATIVE@"> | ||
| #set file_load_section_selected = $file_load_sectionNegative | ||
| #set file_load_section_selected = $acquisition_options.file_load_sectionNegative | ||
| #set polarity="Negative" | ||
| @COMMAND_FILE_LOAD_NEUTRAL@ | ||
| </token> | ||
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@@ -67,31 +65,40 @@ | |
| <when value="no"> | ||
| </when> | ||
| <when value="yes"> | ||
| <conditional name="inputs"> | ||
| <param name="input" type="select" label="Choose your inputs method" > | ||
| <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option> | ||
| <option value="single_file">A mzXML or netCDF file from your history</option> | ||
| </param> | ||
| <when value="zip_file"> | ||
| <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> | ||
| </when> | ||
| <when value="single_file"> | ||
| <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" multiple="true"/> | ||
| </when> | ||
| </conditional> | ||
| <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." /> | ||
| </when> | ||
| </conditional> | ||
| </section> | ||
| </xml> | ||
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| <xml name="test_commun"> | ||
| <section name="getannot"> | ||
| <param name="allowMiss" value="TRUE" /> | ||
| <conditional name="option_toexclude"> | ||
| <param name="option" value="hide" /> | ||
| </conditional> | ||
| </section> | ||
| <section name="db"> | ||
| <param name="kegg_db" value="KEGG" /> | ||
| <param name="ppm_tol" value="8" /> | ||
| </section> | ||
| <section name="export"> | ||
| <param name="prob" value="count" /> | ||
| <param name="html" value="FALSE" /> | ||
| </section> | ||
| <section name="reac2cor"> | ||
| <param name="opt" value="cor" /> | ||
| <param name="corprob" value="0.8" /> | ||
| <param name="pcorprob" value="0.8" /> | ||
| <param name="corths" value="0.75" /> | ||
| </section> | ||
| </xml> | ||
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| <xml name="test_file_load_zip"> | ||
| <section name="file_load_section"> | ||
| <conditional name="file_load_conditional"> | ||
| <param name="file_load_select" value="yes" /> | ||
| <conditional name="inputs"> | ||
| <param name="input" value="zip_file" /> | ||
| <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" /> | ||
| </conditional> | ||
| <param name="input" value="faahKO_reduce.zip" ftype="zip" /> | ||
| </conditional> | ||
| </section> | ||
| </xml> | ||
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@@ -100,10 +107,7 @@ | |
| <section name="file_load_section@POLARITY@"> | ||
| <conditional name="file_load_conditional"> | ||
| <param name="file_load_select" value="yes" /> | ||
| <conditional name="inputs"> | ||
| <param name="input" value="single_file" /> | ||
| <param name="single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> | ||
| </conditional> | ||
| <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> | ||
| </conditional> | ||
| </section> | ||
| </xml> | ||
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@@ -118,7 +122,7 @@ | |
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| .. class:: infomark | ||
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| **Galaxy integration** Misharl Monsoor [email protected] ABIMS TEAM, Station biologique de Roscoff. | ||
| **Galaxy integration** Misharl Monsoor [email protected] (and Gildas Le Corguillé) from ABIMS TEAM, Station biologique de Roscoff. | ||
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| | Contact [email protected] for any questions or concerns about the Galaxy implementation of this tool. | ||
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