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annotate idconvert.xml @ 1:cd33680f08ef draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
author galaxyp
date Sat, 23 Feb 2019 06:19:49 -0500
parents f073fd791784
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f073fd791784 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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1 <tool id="idconvert" name="idconvert" version="@VERSION@.0">
f073fd791784 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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2 <description>Convert mass spectrometry identification files</description>
1
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3 <requirements>
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4 <requirement type="package" version="3.0.9992">proteowizard</requirement>
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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5 </requirements>
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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6 <stdio>
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7 <exit_code range="1:" />
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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8 <regex match="Error"
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9 source="both"
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10 level="fatal"
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11 description="Error" />
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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12 </stdio>
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f073fd791784 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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13 <command>
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14 <![CDATA[
1
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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15 #import os.path
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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16 #set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')])
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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17 ln -s '$from.input' '$input_name' &&
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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18 idconvert '$input_name'
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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19 #if str($to_format) == 'pep.xml':
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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20 --pepXML
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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21 #elif str($to_format) == 'text':
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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22 --text
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23 #end if
cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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24 --outdir 'outdir'
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25 && cp outdir/* '$output'
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26 ]]>
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27 </command>
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28 <inputs>
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29 <conditional name="from">
f073fd791784 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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30 <param name="from_format" type="select" label="Convert from">
f073fd791784 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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31 <option value="mzid">mzIdentML (mzid)</option>
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cd33680f08ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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32 <option value="pepxml">pepXML (pepxml)</option>
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33 <option value="protxml">protXML (protxml)</option>
f073fd791784 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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34 </param>
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35 <when value="mzid">
f073fd791784 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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36 <param name="input" type="data" format="pepxml,protxml,mzid" label="MS mzIdentML (mzid)" />
f073fd791784 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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37 </when>
f073fd791784 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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38 <when value="protxml">
f073fd791784 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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39 <param name="input" type="data" format="protxml" label="MS pepXML (pepxml)" />
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40 <param name="pepxml" type="data" format="pepxml" multiple="true" label="MS Identification" />
0
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41 </when>
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42 <when value="pepxml">
f073fd791784 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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43 <param name="input" type="data" format="pepxml" label="MS Identification" />
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44 </when>
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45 </conditional>
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46 <param name="to_format" type="select" label="Convert to">
f073fd791784 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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47 <option value="mzid">mzIdentML (mzid)</option>
1
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48 <option value="pep.xml">pepXML (pepxml)</option>
0
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49 <option value="text">text</option>
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50 </param>
1
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51 </inputs>
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52 <outputs>
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53 <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}">
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54 <change_format>
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55 <when input="to_format" value="pep.xml" format="pepxml" />
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56 <when input="to_format" value="text" format="txt" />
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57 </change_format>
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58 </data>
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="input" value="Rpal_01.pepXML" />
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63 <param name="from_format" value="pepxml" />
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64 <param name="to_format" value="mzid" />
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65 <output name="output">
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66 <assert_contents>
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67 <has_text text="MzIdentML" />
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68 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
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69 </assert_contents>
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70 </output>
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71 </test>
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72 <test>
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73 <param name="input" value="Rpal_01.mzid" />
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74 <param name="from_format" value="mzid" />
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75 <param name="to_format" value="pep.xml" />
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76 <output name="output">
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77 <assert_contents>
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78 <has_text text="msms_pipeline_analysis" />
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79 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
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80 </assert_contents>
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81 </output>
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82 </test>
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83 </tests>
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84 <help>
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85 <![CDATA[
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86 idconvert [options] [filemasks]
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87 Convert mass spec identification file formats.
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88
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89 Return value: # of failed files.
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90
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91 Options:
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92 -f [ --filelist ] arg : specify text file containing filenames
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93 -o [ --outdir ] arg (=.) : set output directory ('-' for stdout) [.]
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94 -c [ --config ] arg : configuration file (optionName=value)
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95 -e [ --ext ] arg : set extension for output files [mzid|pepXML|txt]
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96 --mzIdentML : write mzIdentML format [default]
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97 --pepXML : write pepXML format
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98 --text : write hierarchical text format
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99 -v [ --verbose ] : display detailed progress information
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100 Examples:
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101
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102 # convert sequest.pepXML to sequest.mzid
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103 idconvert sequest.pepXML
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104
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105 # convert sequest.protXML to sequest.mzid
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106 # Also reads any pepXML file referenced in the
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107 # protXML file if available. If the protXML
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108 # file has been moved from its original location,
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109 # the pepXML will still be found if it has also
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110 # been moved to the same position relative to the
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111 # protXML file. This relative position is determined
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112 # by reading the protXML protein_summary:summary_xml
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113 # and protein_summary_header:source_files values.
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114 idconvert sequest.protXML
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115
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116 # convert mascot.mzid to mascot.pepXML
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117 idconvert mascot.mzid --pepXML
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118
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119 ]]>
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120 </help>
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121 <citations>
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122 <citation type="doi">10.1093/bioinformatics/btn323</citation>
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123 </citations>
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124 </tool>