Mercurial > repos > lecorguille > xcms_group
annotate macros.xml @ 23:dcff3c4a8c80 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5583baab62c0f17cabbfe93ba4f2522e8df9b36b
author | lecorguille |
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date | Thu, 30 Mar 2017 08:34:09 -0400 |
parents | a79d839d625f |
children | 1a7d1f9e8912 |
rev | line source |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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1 <?xml version="1.0"?> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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2 <macros> |
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3 <xml name="requirements"> |
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4 <requirements> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
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5 <requirement type="package" version="0.4_1">r-snow</requirement> |
8ac150e147c9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
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6 <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
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7 <requirement type="package" version="1.1_4">r-batch</requirement> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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8 </requirements> |
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9 </xml> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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10 <xml name="requirements_light"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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11 <requirements> |
f4dc089f9d19
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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12 <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> |
f4dc089f9d19
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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13 </requirements> |
f4dc089f9d19
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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14 </xml> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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15 <xml name="stdio"> |
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16 <stdio> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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17 <exit_code range="1" level="fatal" /> |
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18 </stdio> |
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19 </xml> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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20 |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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21 <token name="@COMMAND_XCMS_SCRIPT@"> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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22 LANG=C Rscript $__tool_directory__/xcms.r |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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23 </token> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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24 |
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25 <token name="@COMMAND_LOG_EXIT@"> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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26 ; |
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27 return=\$?; |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4
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28 mv log.txt '$log'; |
7f667b64d5a5
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4
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29 cat '$log'; |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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30 sh -c "exit \$return" |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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31 </token> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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32 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
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33 <!-- zipfile load for planemo test --> |
8ac150e147c9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
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34 |
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f4dc089f9d19
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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35 <token name="@COMMAND_FILE_LOAD@"> |
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a79d839d625f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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36 #if $file_load_section.file_load_conditional.file_load_select == "yes": |
a79d839d625f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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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"): |
a79d839d625f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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38 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) |
a79d839d625f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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39 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] ) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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40 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4
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41 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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42 #else |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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43 zipfile '$file_load_section.file_load_conditional.input' |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2aff6f6ced8185ed35371d7ad637e5a44f8a250c
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44 #end if |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
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45 #end if |
8ac150e147c9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
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46 </token> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
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47 |
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48 <xml name="input_file_load"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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49 <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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50 <conditional name="file_load_conditional"> |
a79d839d625f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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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." > |
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52 <option value="no" >no need</option> |
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53 <option value="yes" >yes</option> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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54 </param> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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55 <when value="no"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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56 </when> |
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57 <when value="yes"> |
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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." /> |
a79d839d625f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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59 </when> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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60 </conditional> |
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61 </section> |
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62 </xml> |
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63 |
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64 <xml name="test_file_load_zip"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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65 <section name="file_load_section"> |
a79d839d625f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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66 <conditional name="file_load_conditional"> |
a79d839d625f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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67 <param name="file_load_select" value="yes" /> |
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68 <param name="input" value="faahKO_reduce.zip" ftype="zip" /> |
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69 </conditional> |
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70 </section> |
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71 </xml> |
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72 |
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73 <xml name="test_file_load_single"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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74 <section name="file_load_section"> |
a79d839d625f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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75 <conditional name="file_load_conditional"> |
a79d839d625f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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76 <param name="file_load_select" value="yes" /> |
a79d839d625f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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77 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> |
a79d839d625f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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78 </conditional> |
a79d839d625f
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79 </section> |
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80 </xml> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
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81 |
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82 <token name="@COMMAND_PEAKLIST@"> |
a28473761624
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
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83 #if $peaklist.peaklistBool |
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84 variableMetadataOutput '$variableMetadata' |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4
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85 dataMatrixOutput '$dataMatrix' |
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86 convertRTMinute $peaklist.convertRTMinute |
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87 numDigitsMZ $peaklist.numDigitsMZ |
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88 numDigitsRT $peaklist.numDigitsRT |
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89 intval $peaklist.intval |
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90 #end if |
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91 </token> |
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92 |
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93 <xml name="input_peaklist"> |
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94 <conditional name="peaklist"> |
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95 <param name="peaklistBool" type="boolean" label="Get a Peak List" /> |
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96 <when value="true"> |
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97 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> |
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98 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> |
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99 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> |
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100 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> |
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101 <option value="into" selected="true">into</option> |
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102 <option value="maxo">maxo</option> |
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103 <option value="intb">intb</option> |
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104 </param> |
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105 </when> |
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106 <when value="false" /> |
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107 </conditional> |
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108 </xml> |
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109 |
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110 <xml name="output_peaklist"> |
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111 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv"> |
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112 <filter>(peaklist['peaklistBool'])</filter> |
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113 </data> |
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114 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.fillPeaks.dataMatrix.tsv" > |
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115 <filter>(peaklist['peaklistBool'])</filter> |
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116 </data> |
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117 </xml> |
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118 |
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119 <token name="@HELP_AUTHORS@"> |
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120 .. class:: infomark |
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121 |
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122 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu |
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123 |
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124 .. class:: infomark |
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125 |
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126 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] |
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127 |
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128 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. |
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129 |
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130 --------------------------------------------------- |
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131 |
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132 </token> |
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133 |
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134 |
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135 <xml name="citation"> |
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136 <citations> |
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137 <citation type="doi">10.1021/ac051437y</citation> |
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138 <citation type="doi">10.1093/bioinformatics/btu813</citation> |
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139 </citations> |
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140 </xml> |
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141 </macros> |