Mercurial > repos > galaxyp > openms_idmapper

annotate IDMapper.xml @ 13:2517c03f5cd3 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:04:21 +0000
parents 138a734e21a1
children adca857b4884
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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: [ID Processing]-->
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4 <tool id="IDMapper" name="IDMapper" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Assigns protein/peptide identifications to features or consensus features.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDMapper</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 id &&
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20 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
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21 mkdir in &&
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22 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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23 mkdir out &&
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24 #if $spectra._in:
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25 mkdir spectra.in &&
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26 ln -s '$spectra._in' 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)' &&
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27 #end if
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29 ## Main program call
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31 set -o pipefail &&
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32 @EXECUTABLE@ -write_ctd ./ &&
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33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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35 -id
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36 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
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37 -in
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38 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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39 -out
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40 'out/output.${in.ext}'
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41 #if $spectra._in:
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42 -spectra:in
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43 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)'
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44 #end if
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45
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46 ## Postprocessing
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47 && mv 'out/output.${in.ext}' '$out'
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48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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49 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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50 #end if]]></command>
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51 <configfiles>
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52 <inputs name="args_json" data_style="paths"/>
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53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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54 </configfiles>
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55 <inputs>
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56 <param name="id" argument="-id" type="data" format="idxml,mzid" optional="false" label="Protein/peptide identifications file" help=" select idxml,mzid data sets(s)"/>
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57 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,mzq" optional="false" label="Feature map/consensus map file" help=" select consensusxml,featurexml,mzq data sets(s)"/>
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58 <param name="rt_tolerance" argument="-rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
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59 <param name="mz_tolerance" argument="-mz_tolerance" type="float" optional="true" min="0.0" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
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60 <param name="mz_measure" argument="-mz_measure" display="radio" type="select" optional="false" label="Unit of 'mz_tolerance'" help="">
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61 <option value="ppm" selected="true">ppm</option>
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62 <option value="Da">Da</option>
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63 <expand macro="list_string_san"/>
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64 </param>
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65 <param name="mz_reference" argument="-mz_reference" display="radio" type="select" optional="false" label="Source of m/z values for peptide identifications" help="If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',. masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)">
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66 <option value="precursor">precursor</option>
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67 <option value="peptide" selected="true">peptide</option>
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68 <expand macro="list_string_san"/>
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69 </param>
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70 <section name="feature" title="Additional options for featureXML input" help="" expanded="false">
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71 <param name="use_centroid_rt" argument="-feature:use_centroid_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces" help=""/>
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72 <param name="use_centroid_mz" argument="-feature:use_centroid_mz" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces" help="(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)"/>
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73 </section>
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74 <section name="consensus" title="Additional options for consensusXML input" help="" expanded="false">
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75 <param name="use_subelements" argument="-consensus:use_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Match using RT and m/z of sub-features instead of consensus RT and m/z" help="A consensus feature matches if any of its sub-features matches"/>
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76 <param name="annotate_ids_with_subelements" argument="-consensus:annotate_ids_with_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the map index of the sub-feature in the peptide ID" help=""/>
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77 </section>
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78 <section name="spectra" title="Additional options for mzML input" help="" expanded="false">
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79 <param name="_in" argument="-spectra:_in" type="data" format="mzml" optional="true" label="MS run used to annotated unidentified spectra to features or consensus features" help=" select mzml data sets(s)"/>
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80 </section>
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81 <expand macro="adv_opts_macro">
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82 <param name="ignore_charge" argument="-ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" help=""/>
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83 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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84 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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85 <expand macro="list_string_san"/>
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86 </param>
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87 </expand>
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88 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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89 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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90 </param>
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91 </inputs>
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92 <outputs>
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93 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
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94 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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95 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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96 </data>
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97 </outputs>
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98 <tests>
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99 <expand macro="autotest_IDMapper"/>
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100 <expand macro="manutest_IDMapper"/>
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101 </tests>
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102 <help><![CDATA[Assigns protein/peptide identifications to features or consensus features.
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103
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104
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105 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDMapper.html]]></help>
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106 <expand macro="references"/>
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107 </tool>