Mercurial > repos > galaxyp > openms_consensusid

annotate ConsensusID.xml @ 19:91da6dd00bbc draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:45:07 +0000
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1 <!--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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2 <!--Proposed Tool Section: [Identification Processing]-->
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3 <tool id="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Computes a consensus of peptide identifications of several identification engines</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">ConsensusID</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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15 ## Preprocessing
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16 mkdir in_cond.in &&
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17 #if $in_cond.in_select == "no"
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18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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19 ${' '.join(["cp '%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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20 #else
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21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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22 #end if
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23 mkdir out &&
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25 ## Main program call
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27 set -o pipefail &&
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28 @EXECUTABLE@ -write_ctd ./ &&
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29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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31 -in
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32 #if $in_cond.in_select == "no"
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33 ${' '.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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34 #else
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35 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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36 #end if
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37 -out
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38 'out/output.${in_cond.in[0].ext}'
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40 ## Postprocessing
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41 && mv 'out/output.${in_cond.in[0].ext}' '$out'
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42 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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43 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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44 #end if]]></command>
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45 <configfiles>
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46 <inputs name="args_json" data_style="paths"/>
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47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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48 </configfiles>
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49 <inputs>
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50 <conditional name="in_cond">
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51 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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52 <option value="no">No: process all datasets jointly</option>
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53 <option value="yes">Yes: process each dataset in an independent job</option>
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54 </param>
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55 <when value="no">
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56 <param argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="true" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
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57 </when>
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58 <when value="yes">
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59 <param argument="-in" type="data" format="consensusxml,featurexml,idxml" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
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60 </when>
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61 </conditional>
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62 <param argument="-rt_delta" type="float" 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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63 <param argument="-mz_delta" type="float" 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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64 <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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65 <param argument="-algorithm" type="select" 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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66 <option value="PEPMatrix" selected="true">PEPMatrix</option>
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67 <option value="PEPIons">PEPIons</option>
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68 <option value="best">best</option>
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69 <option value="worst">worst</option>
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70 <option value="average">average</option>
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71 <option value="ranks">ranks</option>
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72 <expand macro="list_string_san" name="algorithm"/>
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73 </param>
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74 <section name="filter" title="Options for filtering peptide hits" help="" expanded="false">
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75 <param name="considered_hits" argument="-filter:considered_hits" type="integer" 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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76 <param name="min_support" argument="-filter:min_support" type="float" 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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77 <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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78 <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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79 </section>
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80 <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false">
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81 <param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" 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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82 <param name="min_shared" argument="-PEPIons:min_shared" type="integer" 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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83 </section>
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84 <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false">
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85 <param name="matrix" argument="-PEPMatrix:matrix" type="select" label="Substitution matrix to use for alignment-based similarity scoring" help="">
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86 <option value="identity">identity</option>
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87 <option value="PAM30MS" selected="true">PAM30MS</option>
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88 <expand macro="list_string_san" name="matrix"/>
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89 </param>
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90 <param name="penalty" argument="-PEPMatrix:penalty" type="integer" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help=""/>
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91 </section>
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92 <expand macro="adv_opts_macro">
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93 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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94 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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95 <expand macro="list_string_san" name="test"/>
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96 </param>
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97 </expand>
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98 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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99 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
0
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100 </param>
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101 </inputs>
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102 <outputs>
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103 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
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104 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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105 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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106 </data>
0
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107 </outputs>
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108 <tests>
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109 <!-- 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" value="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 <assert_stdout>
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144 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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145 </assert_stdout>
18
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146 </test>
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147 <!-- TOPP_ConsensusID_2 -->
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148 <test expect_num_outputs="2">
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149 <section name="adv_opts">
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150 <param name="force" value="false"/>
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151 <param name="test" value="true"/>
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152 </section>
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153 <conditional name="in_cond">
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154 <param name="in" value="ConsensusID_2_input.featureXML"/>
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155 </conditional>
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156 <output name="out" value="ConsensusID_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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157 <param name="rt_delta" value="0.1"/>
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158 <param name="mz_delta" value="0.1"/>
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159 <param name="per_spectrum" value="false"/>
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160 <param name="algorithm" value="average"/>
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161 <section name="filter">
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162 <param name="considered_hits" value="0"/>
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163 <param name="min_support" value="0.0"/>
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164 <param name="count_empty" value="false"/>
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165 <param name="keep_old_scores" value="false"/>
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166 </section>
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167 <section name="PEPIons">
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168 <param name="mass_tolerance" value="0.5"/>
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169 <param name="min_shared" value="2"/>
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170 </section>
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171 <section name="PEPMatrix">
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172 <param name="matrix" value="PAM30MS"/>
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173 <param name="penalty" value="5"/>
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174 </section>
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175 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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176 <output name="ctd_out" ftype="xml">
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177 <assert_contents>
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178 <is_valid_xml/>
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179 </assert_contents>
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180 </output>
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181 <assert_stdout>
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182 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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183 </assert_stdout>
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184 </test>
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185 <!-- TOPP_ConsensusID_3 -->
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186 <test expect_num_outputs="2">
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187 <section name="adv_opts">
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188 <param name="force" value="false"/>
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189 <param name="test" value="true"/>
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190 </section>
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191 <conditional name="in_cond">
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192 <param name="in" value="ConsensusID_3_input.consensusXML"/>
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193 </conditional>
19
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194 <output name="out" value="ConsensusID_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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195 <param name="rt_delta" value="0.1"/>
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196 <param name="mz_delta" value="0.1"/>
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197 <param name="per_spectrum" value="false"/>
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198 <param name="algorithm" value="best"/>
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199 <section name="filter">
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200 <param name="considered_hits" value="0"/>
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201 <param name="min_support" value="0.0"/>
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202 <param name="count_empty" value="false"/>
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203 <param name="keep_old_scores" value="false"/>
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204 </section>
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205 <section name="PEPIons">
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206 <param name="mass_tolerance" value="0.5"/>
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207 <param name="min_shared" value="2"/>
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208 </section>
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209 <section name="PEPMatrix">
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210 <param name="matrix" value="PAM30MS"/>
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211 <param name="penalty" value="5"/>
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212 </section>
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213 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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214 <output name="ctd_out" ftype="xml">
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215 <assert_contents>
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216 <is_valid_xml/>
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217 </assert_contents>
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218 </output>
19
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219 <assert_stdout>
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220 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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221 </assert_stdout>
18
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222 </test>
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223 <!-- TOPP_ConsensusID_4 -->
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224 <test expect_num_outputs="2">
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225 <section name="adv_opts">
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226 <param name="force" value="false"/>
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227 <param name="test" value="true"/>
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228 </section>
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229 <conditional name="in_cond">
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230 <param name="in" value="ConsensusID_1_input.idXML"/>
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231 </conditional>
19
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232 <output name="out" value="ConsensusID_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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233 <param name="rt_delta" value="0.1"/>
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234 <param name="mz_delta" value="0.1"/>
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235 <param name="per_spectrum" value="false"/>
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236 <param name="algorithm" value="PEPMatrix"/>
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237 <section name="filter">
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238 <param name="considered_hits" value="6"/>
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239 <param name="min_support" value="0.0"/>
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240 <param name="count_empty" value="false"/>
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241 <param name="keep_old_scores" value="false"/>
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242 </section>
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243 <section name="PEPIons">
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244 <param name="mass_tolerance" value="0.5"/>
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245 <param name="min_shared" value="2"/>
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246 </section>
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247 <section name="PEPMatrix">
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248 <param name="matrix" value="identity"/>
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249 <param name="penalty" value="5"/>
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250 </section>
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251 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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252 <output name="ctd_out" ftype="xml">
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253 <assert_contents>
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254 <is_valid_xml/>
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255 </assert_contents>
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256 </output>
19
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257 <assert_stdout>
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258 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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259 </assert_stdout>
18
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260 </test>
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261 <!-- TOPP_ConsensusID_5 -->
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262 <test expect_num_outputs="2">
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263 <section name="adv_opts">
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264 <param name="force" value="false"/>
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265 <param name="test" value="true"/>
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266 </section>
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267 <conditional name="in_cond">
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268 <param name="in" value="ConsensusID_1_input.idXML"/>
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269 </conditional>
19
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270 <output name="out" value="ConsensusID_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
18
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271 <param name="rt_delta" value="0.1"/>
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272 <param name="mz_delta" value="0.1"/>
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273 <param name="per_spectrum" value="false"/>
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274 <param name="algorithm" value="PEPIons"/>
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275 <section name="filter">
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276 <param name="considered_hits" value="0"/>
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277 <param name="min_support" value="0.0"/>
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278 <param name="count_empty" value="false"/>
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279 <param name="keep_old_scores" value="false"/>
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280 </section>
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281 <section name="PEPIons">
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282 <param name="mass_tolerance" value="0.5"/>
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283 <param name="min_shared" value="2"/>
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284 </section>
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285 <section name="PEPMatrix">
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286 <param name="matrix" value="PAM30MS"/>
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287 <param name="penalty" value="5"/>
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288 </section>
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289 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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290 <output name="ctd_out" ftype="xml">
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291 <assert_contents>
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292 <is_valid_xml/>
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293 </assert_contents>
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294 </output>
19
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295 <assert_stdout>
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296 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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297 </assert_stdout>
18
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298 </test>
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299 <!-- TOPP_ConsensusID_6 -->
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300 <test expect_num_outputs="2">
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301 <section name="adv_opts">
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302 <param name="force" value="false"/>
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303 <param name="test" value="true"/>
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304 </section>
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305 <conditional name="in_cond">
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306 <param name="in" value="ConsensusID_1_input.idXML"/>
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307 </conditional>
19
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308 <output name="out" value="ConsensusID_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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309 <param name="rt_delta" value="0.1"/>
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310 <param name="mz_delta" value="0.1"/>
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311 <param name="per_spectrum" value="false"/>
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312 <param name="algorithm" value="best"/>
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313 <section name="filter">
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314 <param name="considered_hits" value="0"/>
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315 <param name="min_support" value="0.5"/>
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316 <param name="count_empty" value="false"/>
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317 <param name="keep_old_scores" value="false"/>
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318 </section>
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319 <section name="PEPIons">
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320 <param name="mass_tolerance" value="0.5"/>
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321 <param name="min_shared" value="2"/>
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322 </section>
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323 <section name="PEPMatrix">
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324 <param name="matrix" value="PAM30MS"/>
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325 <param name="penalty" value="5"/>
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326 </section>
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327 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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328 <output name="ctd_out" ftype="xml">
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329 <assert_contents>
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330 <is_valid_xml/>
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331 </assert_contents>
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332 </output>
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333 <assert_stdout>
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334 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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335 </assert_stdout>
18
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336 </test>
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337 <!-- TOPP_ConsensusID_7 -->
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338 <test expect_num_outputs="2">
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339 <section name="adv_opts">
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340 <param name="force" value="false"/>
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341 <param name="test" value="true"/>
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342 </section>
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343 <conditional name="in_cond">
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344 <param name="in" value="ConsensusID_6_input.idXML"/>
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345 </conditional>
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346 <output name="out" value="ConsensusID_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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347 <param name="rt_delta" value="0.1"/>
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348 <param name="mz_delta" value="0.1"/>
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349 <param name="per_spectrum" value="true"/>
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350 <param name="algorithm" value="best"/>
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351 <section name="filter">
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352 <param name="considered_hits" value="0"/>
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353 <param name="min_support" value="0.0"/>
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354 <param name="count_empty" value="false"/>
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355 <param name="keep_old_scores" value="true"/>
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356 </section>
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357 <section name="PEPIons">
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358 <param name="mass_tolerance" value="0.5"/>
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359 <param name="min_shared" value="2"/>
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360 </section>
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361 <section name="PEPMatrix">
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362 <param name="matrix" value="PAM30MS"/>
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363 <param name="penalty" value="5"/>
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364 </section>
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365 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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366 <output name="ctd_out" ftype="xml">
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367 <assert_contents>
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368 <is_valid_xml/>
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369 </assert_contents>
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370 </output>
19
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371 <assert_stdout>
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372 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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373 </assert_stdout>
18
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374 </test>
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375 <!-- TOPP_ConsensusID_8 -->
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376 <test expect_num_outputs="2">
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377 <section name="adv_opts">
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378 <param name="force" value="false"/>
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379 <param name="test" value="true"/>
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380 </section>
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381 <conditional name="in_cond">
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382 <param name="in" value="ConsensusID_8_input.idXML"/>
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383 </conditional>
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384 <output name="out" value="ConsensusID_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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385 <param name="rt_delta" value="0.1"/>
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386 <param name="mz_delta" value="0.1"/>
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387 <param name="per_spectrum" value="true"/>
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388 <param name="algorithm" value="best"/>
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389 <section name="filter">
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390 <param name="considered_hits" value="0"/>
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391 <param name="min_support" value="0.0"/>
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392 <param name="count_empty" value="false"/>
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393 <param name="keep_old_scores" value="true"/>
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394 </section>
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395 <section name="PEPIons">
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396 <param name="mass_tolerance" value="0.5"/>
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397 <param name="min_shared" value="2"/>
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398 </section>
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399 <section name="PEPMatrix">
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400 <param name="matrix" value="PAM30MS"/>
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401 <param name="penalty" value="5"/>
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402 </section>
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403 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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404 <output name="ctd_out" ftype="xml">
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405 <assert_contents>
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406 <is_valid_xml/>
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407 </assert_contents>
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408 </output>
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409 <assert_stdout>
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410 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
91da6dd00bbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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411 </assert_stdout>
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f4be248c3d47 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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412 </test>
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413 </tests>
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414 <help><![CDATA[Computes a consensus of peptide identifications of several identification engines.
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415
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416
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417 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ConsensusID.html]]></help>
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418 <expand macro="references"/>
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419 </tool>