Mercurial > repos > galaxyp > openms_idmapper

annotate IDMapper.xml @ 15:adca857b4884 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:05:34 +0000
parents 2517c03f5cd3
children ea02403ff738
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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@VERSION_SUFFIX@" profile="21.05">
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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 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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16 ## Preprocessing
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17 mkdir id &&
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18 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir out &&
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22 #if $spectra._in:
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23 mkdir spectra.in &&
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24 ln -s '$spectra._in' 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)' &&
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25 #end if
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27 ## Main program call
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29 set -o pipefail &&
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30 @EXECUTABLE@ -write_ctd ./ &&
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31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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33 -id
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34 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
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35 -in
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36 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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37 -out
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38 'out/output.${in.ext}'
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39 #if $spectra._in:
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40 -spectra:in
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41 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)'
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42 #end if
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43
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44 ## Postprocessing
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45 && mv 'out/output.${in.ext}' '$out'
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46 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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47 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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48 #end if]]></command>
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49 <configfiles>
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50 <inputs name="args_json" data_style="paths"/>
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51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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52 </configfiles>
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53 <inputs>
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54 <param 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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55 <param 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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56 <param 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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57 <param 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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58 <param argument="-mz_measure" type="select" optional="true" label="Unit of 'mz_tolerance'" help="">
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59 <option value="ppm" selected="true">ppm</option>
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60 <option value="Da">Da</option>
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61 <expand macro="list_string_san" name="mz_measure"/>
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62 </param>
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63 <param argument="-mz_reference" type="select" optional="true" 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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64 <option value="precursor">precursor</option>
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65 <option value="peptide" selected="true">peptide</option>
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66 <expand macro="list_string_san" name="mz_reference"/>
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67 </param>
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68 <section name="feature" title="Additional options for featureXML input" help="" expanded="false">
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69 <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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70 <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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71 </section>
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72 <section name="consensus" title="Additional options for consensusXML input" help="" expanded="false">
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73 <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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74 <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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75 </section>
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76 <section name="spectra" title="Additional options for mzML input" help="" expanded="false">
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77 <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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78 </section>
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79 <expand macro="adv_opts_macro">
15
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80 <param 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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81 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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82 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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83 <expand macro="list_string_san" name="test"/>
11
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84 </param>
0
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85 </expand>
13
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86 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
11
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87 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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88 </param>
0
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89 </inputs>
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90 <outputs>
11
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91 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
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92 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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93 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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94 </data>
0
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95 </outputs>
15
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96 <tests><!-- TOPP_IDMapper_1 -->
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97 <test expect_num_outputs="2">
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98 <section name="adv_opts">
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99 <param name="ignore_charge" value="true"/>
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100 <param name="force" value="false"/>
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101 <param name="test" value="true"/>
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102 </section>
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103 <param name="id" value="IDMapper_1_input.idXML"/>
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104 <param name="in" value="IDMapper_1_input.featureXML"/>
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105 <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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106 <param name="rt_tolerance" value="5.0"/>
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107 <param name="mz_tolerance" value="1.0"/>
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108 <param name="mz_measure" value="Da"/>
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109 <param name="mz_reference" value="precursor"/>
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110 <section name="feature">
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111 <param name="use_centroid_rt" value="false"/>
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112 <param name="use_centroid_mz" value="false"/>
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113 </section>
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114 <section name="consensus">
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115 <param name="use_subelements" value="false"/>
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116 <param name="annotate_ids_with_subelements" value="false"/>
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117 </section>
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118 <section name="spectra"/>
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119 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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120 <output name="ctd_out" ftype="xml">
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121 <assert_contents>
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122 <is_valid_xml/>
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123 </assert_contents>
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124 </output>
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125 </test>
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126 <!-- TOPP_IDMapper_2 -->
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127 <test expect_num_outputs="2">
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128 <section name="adv_opts">
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129 <param name="ignore_charge" value="false"/>
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130 <param name="force" value="false"/>
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131 <param name="test" value="true"/>
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132 </section>
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133 <param name="id" value="IDMapper_2_input.idXML"/>
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134 <param name="in" value="IDMapper_2_input.consensusXML"/>
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135 <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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136 <param name="rt_tolerance" value="5.0"/>
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137 <param name="mz_tolerance" value="1.0"/>
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138 <param name="mz_measure" value="Da"/>
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139 <param name="mz_reference" value="precursor"/>
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140 <section name="feature">
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141 <param name="use_centroid_rt" value="false"/>
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142 <param name="use_centroid_mz" value="true"/>
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143 </section>
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144 <section name="consensus">
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145 <param name="use_subelements" value="false"/>
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146 <param name="annotate_ids_with_subelements" value="false"/>
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147 </section>
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148 <section name="spectra"/>
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149 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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150 <output name="ctd_out" ftype="xml">
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151 <assert_contents>
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152 <is_valid_xml/>
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153 </assert_contents>
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154 </output>
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155 </test>
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156 <!-- TOPP_IDMapper_3 -->
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157 <test expect_num_outputs="2">
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158 <section name="adv_opts">
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159 <param name="ignore_charge" value="true"/>
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160 <param name="force" value="false"/>
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161 <param name="test" value="true"/>
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162 </section>
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163 <param name="id" value="IDMapper_3_input.idXML"/>
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164 <param name="in" value="IDMapper_3_input.featureXML"/>
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165 <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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166 <param name="rt_tolerance" value="4.0"/>
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167 <param name="mz_tolerance" value="3.0"/>
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168 <param name="mz_measure" value="ppm"/>
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169 <param name="mz_reference" value="precursor"/>
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170 <section name="feature">
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171 <param name="use_centroid_rt" value="false"/>
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172 <param name="use_centroid_mz" value="true"/>
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173 </section>
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174 <section name="consensus">
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175 <param name="use_subelements" value="false"/>
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176 <param name="annotate_ids_with_subelements" value="false"/>
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177 </section>
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178 <section name="spectra"/>
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179 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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180 <output name="ctd_out" ftype="xml">
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181 <assert_contents>
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182 <is_valid_xml/>
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183 </assert_contents>
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184 </output>
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185 </test>
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186 <!-- TOPP_IDMapper_4 -->
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187 <test expect_num_outputs="2">
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188 <section name="adv_opts">
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189 <param name="ignore_charge" value="false"/>
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190 <param name="force" value="false"/>
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191 <param name="test" value="true"/>
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192 </section>
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193 <param name="id" value="IDMapper_4_input.idXML"/>
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194 <param name="in" value="IDMapper_4_input.featureXML"/>
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195 <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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196 <param name="rt_tolerance" value="10.0"/>
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197 <param name="mz_tolerance" value="20.0"/>
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198 <param name="mz_measure" value="ppm"/>
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199 <param name="mz_reference" value="peptide"/>
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200 <section name="feature">
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201 <param name="use_centroid_rt" value="false"/>
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202 <param name="use_centroid_mz" value="true"/>
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203 </section>
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204 <section name="consensus">
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205 <param name="use_subelements" value="false"/>
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206 <param name="annotate_ids_with_subelements" value="false"/>
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207 </section>
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208 <section name="spectra">
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209 <param name="_in" value="IDMapper_4_input.mzML"/>
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210 </section>
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211 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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212 <output name="ctd_out" ftype="xml">
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213 <assert_contents>
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214 <is_valid_xml/>
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215 </assert_contents>
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216 </output>
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217 </test>
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218 <!-- TOPP_IDMapper_5 -->
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219 <test expect_num_outputs="2">
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220 <section name="adv_opts">
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221 <param name="ignore_charge" value="false"/>
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222 <param name="force" value="false"/>
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223 <param name="test" value="true"/>
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224 </section>
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225 <param name="id" value="IDMapper_5_input.idXML"/>
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226 <param name="in" value="IDMapper_5_input.featureXML"/>
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227 <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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228 <param name="rt_tolerance" value="20.0"/>
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229 <param name="mz_tolerance" value="10.0"/>
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230 <param name="mz_measure" value="ppm"/>
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231 <param name="mz_reference" value="peptide"/>
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232 <section name="feature">
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233 <param name="use_centroid_rt" value="false"/>
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234 <param name="use_centroid_mz" value="false"/>
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235 </section>
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236 <section name="consensus">
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237 <param name="use_subelements" value="false"/>
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238 <param name="annotate_ids_with_subelements" value="false"/>
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239 </section>
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240 <section name="spectra">
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241 <param name="_in" value="IDMapper_5_input.mzML"/>
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242 </section>
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243 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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244 <output name="ctd_out" ftype="xml">
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245 <assert_contents>
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246 <is_valid_xml/>
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247 </assert_contents>
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248 </output>
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249 </test>
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250 </tests>
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251 <help><![CDATA[Assigns protein/peptide identifications to features or consensus features.
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253
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254 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDMapper.html]]></help>
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255 <expand macro="references"/>
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256 </tool>