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planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
author workflow4metabolomics
date Mon, 11 Sep 2023 22:37:32 +0000
parents ae8de756dfcf
children
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">1.10.0</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">bioconductor-ipo</requirement>
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7 <requirement type="package" version="1.1_5">r-batch</requirement>
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8 </requirements>
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9 </xml>
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11 <token name="@COMMAND_NSLAVES@"><![CDATA[
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12 nSlaves \${GALAXY_SLOTS:-1}
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13 ]]></token>
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15 <!-- zipfile load for planemo test -->
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17 <token name="@ESCAPE_IDENTIFIER@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($single_file.element_identifier))]]></token>
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18 <token name="@COMMAND_FILE_LOAD@"><![CDATA[
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19 #import re
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20 #if $file_load_section.file_load_conditional.file_load_select == "yes":
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21 #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
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22 #set singlefile_sampleName = '|'.join( ["%s" % re.sub('[^\s\w\-\.]', '_', str($single_file.element_identifier)) for single_file in $file_load_section.file_load_conditional.input ] )
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24 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
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25 #end if
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26 ]]></token>
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27
1
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28 <xml name="input_validator_range_integer">
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29 <validator type="regex" message="Should be this format: XX or XX,YY">[0-9]+,?[0-9]*</validator>
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30 </xml>
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32 <xml name="input_validator_range_float">
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33 <validator type="regex" message="Should be one combinaison of those format: XX, XX.YY, XX,YY or XX.XX,YY.YY">[0-9]+[\.]?[0-9]*,?[0-9]*[\.]?[0-9]*</validator>
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34 </xml>
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36 <xml name="input_validator_range_float_neg">
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37 <validator type="regex" message="Should be one combinaison of those format: XX, XX.YY, XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,?[\-]?[0-9]*[\.]?[0-9]*</validator>
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38 </xml>
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40 <xml name="input_file_load">
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41 <section name="file_load_section" title="Resubmit your raw dataset">
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42 <conditional name="file_load_conditional">
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43 <param name="file_load_select" type="select" label="Resubmit your dataset" help="Use only if you get a message which say that your original dataset have been deleted on the server." >
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44 <option value="no" >no need</option>
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45 <option value="yes" >yes</option>
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46 </param>
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47 <when value="no">
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48 </when>
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49 <when value="yes">
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50 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf" 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." />
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51 </when>
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52 </conditional>
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53 </section>
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54 </xml>
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55
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56 <xml name="test_file_load_single">
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57 <section name="file_load_section">
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58 <conditional name="file_load_conditional">
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59 <param name="file_load_select" value="yes" />
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60 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
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61 </conditional>
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62 </section>
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63 </xml>
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64
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65 <token name="@HELP_AUTHORS@"><![CDATA[
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66 .. class:: infomark
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67
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68 **Authors** Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber and Christoph Magnes
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69
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70 .. class:: infomark
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71
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72 **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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73
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74 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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75
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76 ---------------------------------------------------
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77
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78 ]]></token>
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79 <token name="@HELP_NEWVERSION_1_10_0_0@"><![CDATA[
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80 **Version 1.10.0+galaxy0 - 03/09/2019**
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82 - NEW: new versions of the IPO wrappers based on IPO-1.10.0
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83 ]]></token>
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86 <xml name="citation">
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87 <citations>
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88 <citation type="doi">10.1186/s12859-015-0562-8</citation>
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89 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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90 </citations>
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91 </xml>
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92 </macros>