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annotate idconvert.xml @ 1:9e6e840d6b52 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 6674ecccbb39a4bd7e379d6e8969ccec0069c2f1
author galaxyp
date Mon, 08 Aug 2016 10:43:52 -0400
parents 4f7d6bec667f
children edb33e8224c6
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1 <tool id="idconvert" name="idconvert" version="@VERSION@.0">
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2 <description>Convert mass spectrometry identification files</description>
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3 <macros>
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4 <import>msconvert_macros.xml</import>
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5 </macros>
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6 <expand macro="generic_requirements" />
1
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7 <stdio>
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8 <exit_code range="1:" />
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9 <regex match="Error"
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10 source="both"
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11 level="fatal"
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12 description="Error" />
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13 </stdio>
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14 <command>
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15 <![CDATA[
1
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16 #import os.path
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17 #set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')])
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18 ln -s "$from.input" "$input_name" &&
9e6e840d6b52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 6674ecccbb39a4bd7e379d6e8969ccec0069c2f1
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19 idconvert $input_name
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20 #if str($to_format) == 'pep.xml':
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21 --pepXML
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22 #elif str($to_format) == 'text':
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23 --text
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24 #end if
9e6e840d6b52 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 6674ecccbb39a4bd7e379d6e8969ccec0069c2f1
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25 --outdir outdir
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26 && cp outdir/* $output
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27 ]]>
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28 </command>
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29 <inputs>
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30 <conditional name="from">
4f7d6bec667f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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31 <param name="from_format" type="select" label="Convert from">
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32 <option value="mzid">mzIdentML (mzid)</option>
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33 <option value="pepxml">pepXML (pepxml)</option>
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34 <option value="protxml">protXML (protxml)</option>
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35 </param>
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36 <when value="mzid">
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37 <param name="input" type="data" format="pepxml,protxml,mzid" label="MS mzIdentML (mzid)" />
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38 </when>
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39 <when value="protxml">
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40 <param name="input" type="data" format="protxml" label="MS pepXML (pepxml)" />
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41 <param name="pepxml" type="data" format="pepxml" multiple="true" label="MS Identification" />
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42 </when>
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43 <when value="pepxml">
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44 <param name="input" type="data" format="pepxml" label="MS Identification" />
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45 </when>
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46 </conditional>
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47 <param name="to_format" type="select" label="Convert to">
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48 <option value="mzid">mzIdentML (mzid)</option>
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49 <option value="pep.xml">pepXML (pepxml)</option>
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50 <option value="text">text</option>
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51 </param>
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52 </inputs>
1
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53 <outputs>
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54 <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}">
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55 <change_format>
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56 <when input="to_format" value="pep.xml" format="pepxml" />
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57 <when input="to_format" value="text" format="txt" />
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58 </change_format>
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59 </data>
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60 </outputs>
0
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61 <tests>
1
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62 <test>
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63 <param name="input" value="Rpal_01.pepXML" />
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64 <param name="from_format" value="pepxml" />
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65 <param name="to_format" value="mzid" />
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66 <output name="output_psms">
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67 <assert_contents>
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68 <has_text text="MzIdentML" />
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69 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
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70 </assert_contents>
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71 </output>
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72 </test>
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73 <test>
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74 <param name="input" value="Rpal_01.mzid" />
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75 <param name="from_format" value="mzid" />
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76 <param name="to_format" value="pep.xml" />
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77 <output name="output_psms">
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78 <assert_contents>
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79 <has_text text="msms_pipeline_analysis" />
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80 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
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81 </assert_contents>
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82 </output>
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83 </test>
0
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84 </tests>
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85 <help>
1
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86 <![CDATA[
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87 idconvert [options] [filemasks]
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88 Convert mass spec identification file formats.
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89
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90 Return value: # of failed files.
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91
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92 Options:
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93 -f [ --filelist ] arg : specify text file containing filenames
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94 -o [ --outdir ] arg (=.) : set output directory ('-' for stdout) [.]
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95 -c [ --config ] arg : configuration file (optionName=value)
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96 -e [ --ext ] arg : set extension for output files [mzid|pepXML|txt]
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97 --mzIdentML : write mzIdentML format [default]
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98 --pepXML : write pepXML format
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99 --text : write hierarchical text format
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100 -v [ --verbose ] : display detailed progress information
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101 Examples:
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102
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103 # convert sequest.pepXML to sequest.mzid
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104 idconvert sequest.pepXML
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105
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106 # convert sequest.protXML to sequest.mzid
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107 # Also reads any pepXML file referenced in the
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108 # protXML file if available. If the protXML
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109 # file has been moved from its original location,
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110 # the pepXML will still be found if it has also
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111 # been moved to the same position relative to the
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112 # protXML file. This relative position is determined
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113 # by reading the protXML protein_summary:summary_xml
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114 # and protein_summary_header:source_files values.
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115 idconvert sequest.protXML
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116
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117 # convert mascot.mzid to mascot.pepXML
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118 idconvert mascot.mzid --pepXML
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119
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120 ]]>
0
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121 </help>
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122 <expand macro="citations" />
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123 </tool>