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annotate macros.xml @ 2:96debae917e4 draft

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planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit c7a518686137f6d62b7415715152e8d5a9953ed7
author workflow4metabolomics
date Fri, 06 Sep 2019 06:12:08 -0400
parents b60dc620bd14
children ba609408eee9
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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1 <?xml version="1.0"?>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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3 <macros>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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5 <xml name="stdio">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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6 <stdio>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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7 <exit_code range="1" level="fatal" />
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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8 </stdio>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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9 </xml>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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11 <xml name="requirements">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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12 <requirements>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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13 <requirement type="package" version="1.18.1">bioconductor-metams</requirement>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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14 <requirement type="package" version="1.1_4">r-batch</requirement>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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15 <yield />
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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16 </requirements>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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17 </xml>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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19 <xml name="input_file_load">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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20 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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21 <conditional name="file_load_conditional">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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22 <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message saying that your original dataset or zip file have been deleted on the server." >
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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23 <option value="no" >no need</option>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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24 <option value="yes" >yes</option>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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25 </param>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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26 <when value="no">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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27 </when>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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28 <when value="yes">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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29 <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." />
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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30 </when>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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31 </conditional>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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32 </section>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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33 </xml>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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35 <!--<xml name="test_file_load_alg">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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36 <section name="file_load_section">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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37 <conditional name="file_load_conditional">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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38 <param name="file_load_select" value="yes" />
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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39 <param name="input" value="RawFilesTest_alg2_t.mzData,RawFilesTest_alg3_t.mzData,RawFilesTest_alg7_t.mzData,RawFilesTest_alg8_t.mzData,RawFilesTest_alg9_t.mzData,RawFilesTest_alg11_t.mzData" ftype="mzdata" />
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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40 </conditional>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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41 </section>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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42 </xml>-->
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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43
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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44 <xml name="test_file_load_alg_symlink">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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45 <section name="file_load_section">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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46 <conditional name="file_load_conditional">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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47 <param name="file_load_select" value="yes" />
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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48 <param name="input" value="alg2.mzData,alg3.mzData,alg7.mzData,alg8.mzData,alg9.mzData,alg11.mzData" ftype="mzdata" />
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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49 </conditional>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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50 </section>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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51 </xml>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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52
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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53 <!-- COMMAND -->
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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54 <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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55
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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56 <token name="@COMMAND_LOG_EXIT@">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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57 ;
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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58 return=\$?;
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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59 cat 'log.txt';
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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60 sh -c "exit \$return"
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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61 </token>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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62
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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63 <!-- FILE_LOAD for planemo test -->
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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64 <!-- Change | for , because I use it in metaMS tool -->
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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65 <token name="@COMMAND_FILE_LOAD@">
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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66 #if $file_load_section.file_load_conditional.file_load_select == "yes":
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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67 #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"):
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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68 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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69 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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70
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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71 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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72 #else
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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73 zipfile '$file_load_section.file_load_conditional.input'
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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74 #end if
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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75 #end if
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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76 </token>
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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77
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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78 </macros>