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annotate macros.xml @ 25:230f0bc9e792 draft

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author lecorguille
date Fri, 10 Feb 2017 11:11:27 -0500
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children 591d26b9027e
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="0.4_1">r-snow</requirement>
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6 <requirement type="package" version="1.26.0">bioconductor-camera</requirement>
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7 <requirement type="package" version="2.26.0">bioconductor-multtest</requirement>
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8 <requirement type="package" version="1.1_4">r-batch</requirement>
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9 <requirement type="package" version="1.6.27">libpng</requirement>
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10 <requirement type="package" version="1.3.20">graphicsmagick</requirement>
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11 </requirements>
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12 </xml>
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13 <xml name="stdio">
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14 <stdio>
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15 <exit_code range="1" level="fatal" />
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16 </stdio>
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17 </xml>
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19 <token name="@COMMAND_CAMERA_SCRIPT@">
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20 LANG=C Rscript $__tool_directory__/CAMERA.r
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21 </token>
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22
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23 <!-- zipfile load for planemo test -->
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24 <token name="@COMMAND_FILE_LOAD@">
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25 #if $file_load_conditional.file_load_select == "yes":
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26 #if $file_load_conditional.inputs.input == "zip_file":
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27 zipfile '$file_load_conditional.inputs.zip_file'
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28 #else
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29 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] )
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30 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] )
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31
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32 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
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33 #end if
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34 #end if
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35 </token>
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36
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37 <xml name="file_load">
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38 <conditional name="file_load_conditional">
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39 <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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40 <option value="no" >no need</option>
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41 <option value="yes" >yes</option>
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42 </param>
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43 <when value="no">
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44 </when>
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45 <when value="yes">
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46 <conditional name="inputs">
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47 <param name="input" type="select" label="Choose your inputs method" >
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48 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
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49 <option value="single_file">A mzXML or netCDF file from your history</option>
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50 </param>
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51 <when value="zip_file">
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52 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
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53 </when>
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54 <when value="single_file">
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55 <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" multiple="true"/>
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56 </when>
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57 </conditional>
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58 </when>
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59 </conditional>
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60 </xml>
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61
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62 <token name="@COMMAND_PEAKLIST@">
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63 convertRTMinute $convertRTMinute
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64 numDigitsMZ $numDigitsMZ
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65 numDigitsRT $numDigitsRT
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66 intval $intval
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67 </token>
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68
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69 <xml name="input_peaklist">
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70 <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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71 <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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72 <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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73 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
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74 <option value="into" selected="true">into</option>
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75 <option value="maxo" >maxo</option>
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76 <option value="intb">intb</option>
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77 </param>
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78 </xml>
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79
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80 <token name="@HELP_AUTHORS@">
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81 .. class:: infomark
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82
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83 **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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84
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85 .. class:: infomark
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86
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87 **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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88
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89 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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90
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91 ---------------------------------------------------
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92
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93 </token>
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94
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95
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96 <xml name="citation">
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97 <citations>
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98 <citation type="doi">10.1021/ac202450g</citation>
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99 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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100 </citations>
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101 </xml>
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102 </macros>