Mercurial > repos > galaxyp > openms_consensusid

annotate ConsensusID.xml @ 18:f4be248c3d47 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 19:03:29 +0000
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children 91da6dd00bbc
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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="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Computes a consensus of peptide identifications of several identification engines.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ConsensusID</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 in_cond.in &&
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18 #if $in_cond.in_select == "no"
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19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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21 #else
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22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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23 #end if
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24 mkdir out &&
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26 ## Main program call
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27
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28 set -o pipefail &&
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29 @EXECUTABLE@ -write_ctd ./ &&
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30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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32 -in
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33 #if $in_cond.in_select == "no"
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34 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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35 #else
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36 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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37 #end if
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38 -out
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39 'out/output.${in_cond.in[0].ext}'
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41 ## Postprocessing
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42 && mv 'out/output.${in_cond.in[0].ext}' '$out'
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43 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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44 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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45 #end if]]></command>
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46 <configfiles>
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47 <inputs name="args_json" data_style="paths"/>
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48 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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49 </configfiles>
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50 <inputs>
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51 <conditional name="in_cond">
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52 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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53 <option value="no">No: process all datasets jointly</option>
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54 <option value="yes">Yes: process each dataset in an independent job</option>
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55 </param>
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56 <when value="no">
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57 <param argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="true" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
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58 </when>
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59 <when value="yes">
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60 <param argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="false" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
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61 </when>
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62 </conditional>
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63 <param argument="-rt_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help=""/>
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64 <param argument="-mz_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help=""/>
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65 <param argument="-per_spectrum" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(only idXML) if set, mapping will be done based on exact matching of originating mzml file and spectrum_ref" help=""/>
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66 <param argument="-algorithm" type="select" optional="true" label="Algorithm used for consensus scoring" help="* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores.. * PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores.. * best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs.. * worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs.. * average: For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs.. * ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types">
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67 <option value="PEPMatrix" selected="true">PEPMatrix</option>
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68 <option value="PEPIons">PEPIons</option>
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69 <option value="best">best</option>
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70 <option value="worst">worst</option>
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71 <option value="average">average</option>
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72 <option value="ranks">ranks</option>
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73 <expand macro="list_string_san" name="algorithm"/>
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74 </param>
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75 <section name="filter" title="Options for filtering peptide hits" help="" expanded="false">
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76 <param name="considered_hits" argument="-filter:considered_hits" type="integer" optional="true" min="0" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help=""/>
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77 <param name="min_support" argument="-filter:min_support" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help=""/>
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78 <param name="count_empty" argument="-filter:count_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Count empty ID runs" help="(i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?"/>
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79 <param name="keep_old_scores" argument="-filter:keep_old_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set, keeps the original scores as user params" help=""/>
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80 </section>
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81 <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false">
18
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82 <param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" optional="true" min="0.0" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help=""/>
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83 <param name="min_shared" argument="-PEPIons:min_shared" type="integer" optional="true" min="1" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/>
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84 </section>
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85 <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false">
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86 <param name="matrix" argument="-PEPMatrix:matrix" type="select" optional="true" label="Substitution matrix to use for alignment-based similarity scoring" help="">
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87 <option value="identity">identity</option>
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88 <option value="PAM30MS" selected="true">PAM30MS</option>
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89 <expand macro="list_string_san" name="matrix"/>
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90 </param>
18
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91 <param name="penalty" argument="-PEPMatrix:penalty" type="integer" optional="true" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help=""/>
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92 </section>
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93 <expand macro="adv_opts_macro">
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94 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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95 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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96 <expand macro="list_string_san" name="test"/>
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97 </param>
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98 </expand>
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99 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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100 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
0
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101 </param>
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102 </inputs>
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103 <outputs>
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104 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
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105 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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106 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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107 </data>
0
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108 </outputs>
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109 <tests><!-- TOPP_ConsensusID_1 -->
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110 <test expect_num_outputs="2">
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111 <section name="adv_opts">
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112 <param name="force" value="false"/>
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113 <param name="test" value="true"/>
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114 </section>
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115 <conditional name="in_cond">
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116 <param name="in" value="ConsensusID_1_input.idXML"/>
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117 </conditional>
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118 <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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119 <param name="rt_delta" value="0.1"/>
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120 <param name="mz_delta" value="0.1"/>
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121 <param name="per_spectrum" value="false"/>
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122 <param name="algorithm" value="PEPMatrix"/>
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123 <section name="filter">
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124 <param name="considered_hits" value="0"/>
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125 <param name="min_support" value="0.0"/>
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126 <param name="count_empty" value="false"/>
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127 <param name="keep_old_scores" value="false"/>
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128 </section>
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129 <section name="PEPIons">
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130 <param name="mass_tolerance" value="0.5"/>
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131 <param name="min_shared" value="2"/>
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132 </section>
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133 <section name="PEPMatrix">
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134 <param name="matrix" value="PAM30MS"/>
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135 <param name="penalty" value="5"/>
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136 </section>
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137 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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138 <output name="ctd_out" ftype="xml">
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139 <assert_contents>
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140 <is_valid_xml/>
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141 </assert_contents>
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142 </output>
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143 </test>
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144 <!-- TOPP_ConsensusID_2 -->
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145 <test expect_num_outputs="2">
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146 <section name="adv_opts">
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147 <param name="force" value="false"/>
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148 <param name="test" value="true"/>
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149 </section>
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150 <conditional name="in_cond">
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151 <param name="in" value="ConsensusID_2_input.featureXML"/>
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152 </conditional>
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153 <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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154 <param name="rt_delta" value="0.1"/>
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155 <param name="mz_delta" value="0.1"/>
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156 <param name="per_spectrum" value="false"/>
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157 <param name="algorithm" value="average"/>
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158 <section name="filter">
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159 <param name="considered_hits" value="0"/>
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160 <param name="min_support" value="0.0"/>
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161 <param name="count_empty" value="false"/>
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162 <param name="keep_old_scores" value="false"/>
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163 </section>
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164 <section name="PEPIons">
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165 <param name="mass_tolerance" value="0.5"/>
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166 <param name="min_shared" value="2"/>
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167 </section>
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168 <section name="PEPMatrix">
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169 <param name="matrix" value="PAM30MS"/>
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170 <param name="penalty" value="5"/>
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171 </section>
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172 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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173 <output name="ctd_out" ftype="xml">
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174 <assert_contents>
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175 <is_valid_xml/>
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176 </assert_contents>
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177 </output>
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178 </test>
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179 <!-- TOPP_ConsensusID_3 -->
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180 <test expect_num_outputs="2">
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181 <section name="adv_opts">
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182 <param name="force" value="false"/>
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183 <param name="test" value="true"/>
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184 </section>
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185 <conditional name="in_cond">
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186 <param name="in" value="ConsensusID_3_input.consensusXML"/>
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187 </conditional>
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188 <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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189 <param name="rt_delta" value="0.1"/>
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190 <param name="mz_delta" value="0.1"/>
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191 <param name="per_spectrum" value="false"/>
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192 <param name="algorithm" value="best"/>
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193 <section name="filter">
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194 <param name="considered_hits" value="0"/>
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195 <param name="min_support" value="0.0"/>
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196 <param name="count_empty" value="false"/>
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197 <param name="keep_old_scores" value="false"/>
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198 </section>
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199 <section name="PEPIons">
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200 <param name="mass_tolerance" value="0.5"/>
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201 <param name="min_shared" value="2"/>
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202 </section>
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203 <section name="PEPMatrix">
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204 <param name="matrix" value="PAM30MS"/>
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205 <param name="penalty" value="5"/>
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206 </section>
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207 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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208 <output name="ctd_out" ftype="xml">
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209 <assert_contents>
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210 <is_valid_xml/>
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211 </assert_contents>
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212 </output>
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213 </test>
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214 <!-- TOPP_ConsensusID_4 -->
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215 <test expect_num_outputs="2">
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216 <section name="adv_opts">
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217 <param name="force" value="false"/>
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218 <param name="test" value="true"/>
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219 </section>
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220 <conditional name="in_cond">
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221 <param name="in" value="ConsensusID_1_input.idXML"/>
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222 </conditional>
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223 <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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224 <param name="rt_delta" value="0.1"/>
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225 <param name="mz_delta" value="0.1"/>
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226 <param name="per_spectrum" value="false"/>
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227 <param name="algorithm" value="PEPMatrix"/>
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228 <section name="filter">
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229 <param name="considered_hits" value="6"/>
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230 <param name="min_support" value="0.0"/>
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231 <param name="count_empty" value="false"/>
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232 <param name="keep_old_scores" value="false"/>
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233 </section>
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234 <section name="PEPIons">
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235 <param name="mass_tolerance" value="0.5"/>
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236 <param name="min_shared" value="2"/>
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237 </section>
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238 <section name="PEPMatrix">
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239 <param name="matrix" value="identity"/>
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240 <param name="penalty" value="5"/>
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241 </section>
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242 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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243 <output name="ctd_out" ftype="xml">
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244 <assert_contents>
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245 <is_valid_xml/>
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246 </assert_contents>
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247 </output>
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248 </test>
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249 <!-- TOPP_ConsensusID_5 -->
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250 <test expect_num_outputs="2">
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251 <section name="adv_opts">
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252 <param name="force" value="false"/>
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253 <param name="test" value="true"/>
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254 </section>
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255 <conditional name="in_cond">
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256 <param name="in" value="ConsensusID_1_input.idXML"/>
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257 </conditional>
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258 <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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259 <param name="rt_delta" value="0.1"/>
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260 <param name="mz_delta" value="0.1"/>
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261 <param name="per_spectrum" value="false"/>
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262 <param name="algorithm" value="PEPIons"/>
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263 <section name="filter">
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264 <param name="considered_hits" value="0"/>
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265 <param name="min_support" value="0.0"/>
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266 <param name="count_empty" value="false"/>
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267 <param name="keep_old_scores" value="false"/>
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268 </section>
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269 <section name="PEPIons">
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270 <param name="mass_tolerance" value="0.5"/>
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271 <param name="min_shared" value="2"/>
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272 </section>
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273 <section name="PEPMatrix">
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274 <param name="matrix" value="PAM30MS"/>
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275 <param name="penalty" value="5"/>
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276 </section>
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277 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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278 <output name="ctd_out" ftype="xml">
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279 <assert_contents>
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280 <is_valid_xml/>
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281 </assert_contents>
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282 </output>
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283 </test>
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284 <!-- TOPP_ConsensusID_6 -->
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285 <test expect_num_outputs="2">
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286 <section name="adv_opts">
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287 <param name="force" value="false"/>
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288 <param name="test" value="true"/>
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289 </section>
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290 <conditional name="in_cond">
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291 <param name="in" value="ConsensusID_1_input.idXML"/>
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292 </conditional>
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293 <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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294 <param name="rt_delta" value="0.1"/>
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295 <param name="mz_delta" value="0.1"/>
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296 <param name="per_spectrum" value="false"/>
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297 <param name="algorithm" value="best"/>
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298 <section name="filter">
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299 <param name="considered_hits" value="0"/>
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300 <param name="min_support" value="0.5"/>
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301 <param name="count_empty" value="false"/>
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302 <param name="keep_old_scores" value="false"/>
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303 </section>
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304 <section name="PEPIons">
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305 <param name="mass_tolerance" value="0.5"/>
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306 <param name="min_shared" value="2"/>
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307 </section>
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308 <section name="PEPMatrix">
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309 <param name="matrix" value="PAM30MS"/>
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310 <param name="penalty" value="5"/>
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311 </section>
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312 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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313 <output name="ctd_out" ftype="xml">
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314 <assert_contents>
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315 <is_valid_xml/>
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316 </assert_contents>
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317 </output>
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318 </test>
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319 <!-- TOPP_ConsensusID_7 -->
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320 <test expect_num_outputs="2">
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321 <section name="adv_opts">
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322 <param name="force" value="false"/>
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323 <param name="test" value="true"/>
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324 </section>
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325 <conditional name="in_cond">
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326 <param name="in" value="ConsensusID_6_input.idXML"/>
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327 </conditional>
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328 <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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329 <param name="rt_delta" value="0.1"/>
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330 <param name="mz_delta" value="0.1"/>
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331 <param name="per_spectrum" value="true"/>
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332 <param name="algorithm" value="best"/>
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333 <section name="filter">
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334 <param name="considered_hits" value="0"/>
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335 <param name="min_support" value="0.0"/>
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336 <param name="count_empty" value="false"/>
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337 <param name="keep_old_scores" value="true"/>
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338 </section>
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339 <section name="PEPIons">
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340 <param name="mass_tolerance" value="0.5"/>
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341 <param name="min_shared" value="2"/>
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342 </section>
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343 <section name="PEPMatrix">
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344 <param name="matrix" value="PAM30MS"/>
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345 <param name="penalty" value="5"/>
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346 </section>
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347 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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348 <output name="ctd_out" ftype="xml">
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349 <assert_contents>
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350 <is_valid_xml/>
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351 </assert_contents>
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352 </output>
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353 </test>
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354 <!-- TOPP_ConsensusID_8 -->
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355 <test expect_num_outputs="2">
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356 <section name="adv_opts">
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357 <param name="force" value="false"/>
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358 <param name="test" value="true"/>
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359 </section>
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360 <conditional name="in_cond">
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361 <param name="in" value="ConsensusID_8_input.idXML"/>
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362 </conditional>
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363 <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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364 <param name="rt_delta" value="0.1"/>
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365 <param name="mz_delta" value="0.1"/>
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366 <param name="per_spectrum" value="true"/>
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367 <param name="algorithm" value="best"/>
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368 <section name="filter">
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369 <param name="considered_hits" value="0"/>
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370 <param name="min_support" value="0.0"/>
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371 <param name="count_empty" value="false"/>
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372 <param name="keep_old_scores" value="true"/>
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373 </section>
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374 <section name="PEPIons">
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375 <param name="mass_tolerance" value="0.5"/>
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376 <param name="min_shared" value="2"/>
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377 </section>
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378 <section name="PEPMatrix">
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379 <param name="matrix" value="PAM30MS"/>
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380 <param name="penalty" value="5"/>
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381 </section>
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382 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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383 <output name="ctd_out" ftype="xml">
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384 <assert_contents>
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385 <is_valid_xml/>
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386 </assert_contents>
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387 </output>
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388 </test>
13
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389 </tests>
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390 <help><![CDATA[Computes a consensus of peptide identifications of several identification engines.
0
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391
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392
18
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393 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ConsensusID.html]]></help>
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394 <expand macro="references"/>
0
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395 </tool>