Mercurial > repos > galaxyp > openms_msstatsconverter

annotate MSstatsConverter.xml @ 1:80eb149b1579 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 12:18:04 +0000
parents 0dcd11bc33f8
children e444b158fb20
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0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MSstatsConverter" name="MSstatsConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Converter to input for MSstats</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MSstatsConverter</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir in_design &&
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22 ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
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23 mkdir out &&
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24 #if $adv_opts_cond.adv_opts_selector=='advanced':
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25 #if $adv_opts_cond.reannotate_filenames:
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26 mkdir adv_opts_cond.reannotate_filenames &&
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27 ${ ' '.join(["ln -s '%s' 'adv_opts_cond.reannotate_filenames/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $adv_opts_cond.reannotate_filenames if _]) }
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28 #end if
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29 #end if
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30
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 ## Main program call
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32
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33 set -o pipefail &&
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34 @EXECUTABLE@ -write_ctd ./ &&
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35 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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36 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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37 -in
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38 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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39 -in_design
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40 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)'
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41 -out
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42 'out/output.${gxy2omsext("csv")}'
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43 #if $adv_opts_cond.adv_opts_selector=='advanced':
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44 #if $adv_opts_cond.reannotate_filenames:
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45 -reannotate_filenames
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46 ${' '.join(["'adv_opts_cond.reannotate_filenames/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $adv_opts_cond.reannotate_filenames if _])}
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47 #end if
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48 #end if
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49
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50 ## Postprocessing
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51 && mv 'out/output.${gxy2omsext("csv")}' '$out'
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52 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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53 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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54 #end if]]></command>
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55 <configfiles>
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56 <inputs name="args_json" data_style="paths"/>
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57 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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58 </configfiles>
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59 <inputs>
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60 <param name="in" argument="-in" type="data" format="consensusxml" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
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61 <param name="in_design" argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/>
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62 <param name="method" argument="-method" display="radio" type="select" optional="false" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help="">
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63 <option value="LFQ" selected="true">LFQ</option>
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64 <option value="ISO">ISO</option>
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65 <expand macro="list_string_san"/>
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66 </param>
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67 <param name="msstats_bioreplicate" argument="-msstats_bioreplicate" type="text" optional="true" value="MSstats_BioReplicate" label="Which column in the condition table should be used for MSstats 'BioReplicate'" help="">
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68 <expand macro="list_string_san"/>
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69 </param>
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70 <param name="msstats_condition" argument="-msstats_condition" type="text" optional="true" value="MSstats_Condition" label="Which column in the condition table should be used for MSstats 'Condition'" help="">
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71 <expand macro="list_string_san"/>
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72 </param>
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73 <param name="msstats_mixture" argument="-msstats_mixture" type="text" optional="true" value="MSstats_Mixture" label="Which column in the condition table should be used for MSstats 'Mixture'" help="">
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74 <expand macro="list_string_san"/>
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75 </param>
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76 <param name="labeled_reference_peptides" argument="-labeled_reference_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, IsotopeLabelType is 'H', else 'L'" help=""/>
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77 <expand macro="adv_opts_macro">
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78 <param name="reannotate_filenames" argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
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79 <param name="retention_time_summarization_method" argument="-retention_time_summarization_method" type="select" optional="false" label="How indistinguishable peptidoforms at different retention times should be treated" help="This is usually necessary for LFQ experiments and therefore defaults to 'max'. In case of TMT/iTRAQ, MSstatsTMT does the aggregation itself later and the parameter always resets to manual (i.e. is unused)">
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80 <option value="manual">manual</option>
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81 <option value="max" selected="true">max</option>
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82 <option value="min">min</option>
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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83 <option value="mean">mean</option>
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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84 <option value="sum">sum</option>
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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85 <expand macro="list_string_san"/>
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86 </param>
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87 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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88 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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89 <expand macro="list_string_san"/>
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90 </param>
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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91 </expand>
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92 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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93 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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94 </param>
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95 </inputs>
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96 <outputs>
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97 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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98 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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99 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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100 </data>
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101 </outputs>
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102 <tests>
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103 <expand macro="autotest_MSstatsConverter"/>
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104 <expand macro="manutest_MSstatsConverter"/>
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105 </tests>
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106 <help><![CDATA[Converter to input for MSstats
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107
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108
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109 For more information, visit http://www.openms.de/documentation/UTILS_MSstatsConverter.html]]></help>
0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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110 <expand macro="references"/>
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111 </tool>