Mercurial > repos > mmonsoor > probmetab
diff macros.xml @ 3:abcfa1648b66 draft
planemo upload commit c897279aa8cae0a4ad889bb05b143f32d2b6d712
| author | lecorguille |
|---|---|
| date | Fri, 07 Apr 2017 07:14:12 -0400 |
| parents | 3a9914b37f2f |
| children |
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--- a/macros.xml Mon Jul 04 11:58:10 2016 -0400 +++ b/macros.xml Fri Apr 07 07:14:12 2017 -0400 @@ -16,29 +16,102 @@ <token name="@COMMAND_CAMERA_SCRIPT@"> LANG=C Rscript $__tool_directory__/probmetab.r </token> - - <!-- zipfile load for planemo test --> - <token name="@COMMAND_ZIPFILE_LOAD@"> - #if $zipfile_load_conditional.zipfile_load_select == "yes": - #if $zipfile_load_conditional.zip_file: - zipfile $zipfile_load_conditional.zip_file + + <token name="@COMMAND_LOG_EXIT@"> + ; + return=\$?; + cat 'log.txt'; + sh -c "exit \$return" + </token> + + <!-- 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.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 '$singlefile_sampleName' + #else + zipfile$polarity '$file_load_section_selected.file_load_conditional.input' #end if - #end if + #end if + </token> + + <token name="@COMMAND_FILE_LOAD_ONE@"> + #set file_load_section_selected = $acquisition_options.file_load_section + #set polarity="" + @COMMAND_FILE_LOAD_NEUTRAL@ + </token> + + <token name="@COMMAND_FILE_LOAD_POSITIVE@"> + #set file_load_section_selected = $acquisition_options.file_load_sectionPositive + #set polarity="Positive" + @COMMAND_FILE_LOAD_NEUTRAL@ + </token> + + <token name="@COMMAND_FILE_LOAD_NEGATIVE@"> + #set file_load_section_selected = $acquisition_options.file_load_sectionNegative + #set polarity="Negative" + @COMMAND_FILE_LOAD_NEUTRAL@ </token> - <xml name="zipfile_load"> - <conditional name="zipfile_load_conditional"> - <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." > - <option value="no" >no need</option> - <option value="yes" selected="peakgroups">yes</option> - </param> - <when value="no"> - </when> - <when value="yes"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> - </when> - </conditional> + + <xml name="input_file_load" token_polarity=""> + <section name="file_load_section@POLARITY@" title="@POLARITY@ Resubmit your raw dataset or your zip file"> + <conditional name="file_load_conditional"> + <param name="file_load_select" type="select" label="@POLARITY@ Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." > + <option value="no" >no need</option> + <option value="yes" >yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <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> - + + <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> + + <xml name="test_file_load_zip"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="faahKO_reduce.zip" ftype="zip" /> + </conditional> + </section> + </xml> + + <xml name="test_file_load_single" token_polarity="">> + <section name="file_load_section@POLARITY@"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> + </conditional> + </section> + </xml> + <token name="@HELP_AUTHORS@"> .. class:: infomark @@ -49,7 +122,7 @@ .. class:: infomark -**Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABIMS TEAM, Station biologique de Roscoff. +**Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr (and Gildas Le Corguillé) from ABIMS TEAM, Station biologique de Roscoff. | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.