Mercurial > repos > lecorguille > xcms_fillpeaks
comparison macros.xml @ 23:7e289788d37d draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
| author | lecorguille |
|---|---|
| date | Wed, 01 Mar 2017 16:58:07 -0500 |
| parents | a6938c381d4e |
| children | 0544bc5967ed |
comparison
equal
deleted
inserted
replaced
| 22:a6938c381d4e | 23:7e289788d37d |
|---|---|
| 31 </token> | 31 </token> |
| 32 | 32 |
| 33 <!-- zipfile load for planemo test --> | 33 <!-- zipfile load for planemo test --> |
| 34 | 34 |
| 35 <token name="@COMMAND_FILE_LOAD@"> | 35 <token name="@COMMAND_FILE_LOAD@"> |
| 36 #if $file_load_conditional.file_load_select == "yes": | 36 #if $file_load_section.file_load_conditional.file_load_select == "yes": |
| 37 #if $file_load_conditional.inputs.input == "zip_file": | 37 #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"): |
| 38 zipfile '$file_load_conditional.inputs.zip_file' | 38 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) |
| 39 #else | 39 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] ) |
| 40 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] ) | |
| 41 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] ) | |
| 42 | 40 |
| 43 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' | 41 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' |
| 42 #else | |
| 43 zipfile '$file_load_section.file_load_conditional.input' | |
| 44 #end if | 44 #end if |
| 45 #end if | 45 #end if |
| 46 </token> | 46 </token> |
| 47 | 47 |
| 48 <xml name="file_load"> | 48 <xml name="input_file_load"> |
| 49 <conditional name="file_load_conditional"> | 49 <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> |
| 50 <param name="file_load_select" type="select" label="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." > | 50 <conditional name="file_load_conditional"> |
| 51 <option value="no" >no need</option> | 51 <param name="file_load_select" type="select" label="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." > |
| 52 <option value="yes" >yes</option> | 52 <option value="no" >no need</option> |
| 53 </param> | 53 <option value="yes" >yes</option> |
| 54 <when value="no"> | 54 </param> |
| 55 </when> | 55 <when value="no"> |
| 56 <when value="yes"> | 56 </when> |
| 57 <conditional name="inputs"> | 57 <when value="yes"> |
| 58 <param name="input" type="select" label="Choose your inputs method" > | 58 <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." /> |
| 59 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option> | 59 </when> |
| 60 <option value="single_file">A mzXML or netCDF file from your history</option> | 60 </conditional> |
| 61 </param> | 61 </section> |
| 62 <when value="zip_file"> | 62 </xml> |
| 63 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> | 63 |
| 64 </when> | 64 <xml name="test_file_load_zip"> |
| 65 <when value="single_file"> | 65 <section name="file_load_section"> |
| 66 <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" multiple="true"/> | 66 <conditional name="file_load_conditional"> |
| 67 </when> | 67 <param name="file_load_select" value="yes" /> |
| 68 </conditional> | 68 <param name="input" value="faahKO_reduce.zip" ftype="zip" /> |
| 69 </when> | 69 </conditional> |
| 70 </conditional> | 70 </section> |
| 71 </xml> | |
| 72 | |
| 73 <xml name="test_file_load_single"> | |
| 74 <section name="file_load_section"> | |
| 75 <conditional name="file_load_conditional"> | |
| 76 <param name="file_load_select" value="yes" /> | |
| 77 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> | |
| 78 </conditional> | |
| 79 </section> | |
| 71 </xml> | 80 </xml> |
| 72 | 81 |
| 73 <token name="@COMMAND_PEAKLIST@"> | 82 <token name="@COMMAND_PEAKLIST@"> |
| 74 #if $peaklist.peaklistBool | 83 #if $peaklist.peaklistBool |
| 75 variableMetadataOutput '$variableMetadata' | 84 variableMetadataOutput '$variableMetadata' |