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comparison PercolatorAdapter.xml @ 8:016964c597f5 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 18:56:56 +0000
parents 147aaac03456
children 02796e3ddec1
comparison
equal deleted inserted replaced
7:0fc9ae55bcfc 8:016964c597f5
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="PercolatorAdapter" name="PercolatorAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="PercolatorAdapter" name="PercolatorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Facilitate input to Percolator and reintegrate.</description> 5 <description>Facilitate input to Percolator and reintegrate.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PercolatorAdapter</token> 7 <token name="@EXECUTABLE@">PercolatorAdapter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
16 #import re 14 #import re
17 15
18 ## Preprocessing 16 ## Preprocessing
19 #if $in: 17 #if $in_cond.in:
20 mkdir in && 18 mkdir in_cond.in &&
21 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 19 #if $in_cond.in_select == "no"
22 #end if 20 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
23 #if $in_decoy: 21 ${' '.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])}
24 mkdir in_decoy && 22 #else
25 ${ ' '.join(["ln -s '%s' 'in_decoy/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_decoy if _]) } 23 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
24 #end if
25 #end if
26 #if $in_decoy_cond.in_decoy:
27 mkdir in_decoy_cond.in_decoy &&
28 #if $in_decoy_cond.in_decoy_select == "no"
29 mkdir ${' '.join(["'in_decoy_cond.in_decoy/%s'" % (i) for i, f in enumerate($in_decoy_cond.in_decoy) if f])} &&
30 ${' '.join(["ln -s '%s' 'in_decoy_cond.in_decoy/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_decoy_cond.in_decoy) if f])}
31 #else
32 ln -s '$in_decoy_cond.in_decoy' 'in_decoy_cond.in_decoy/${re.sub("[^\w\-_]", "_", $in_decoy_cond.in_decoy.element_identifier)}.$gxy2omsext($in_decoy_cond.in_decoy.ext)' &&
33 #end if
26 #end if 34 #end if
27 #if $in_osw: 35 #if $in_osw:
28 mkdir in_osw && 36 mkdir in_osw &&
29 ln -s '$in_osw' 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)' && 37 ln -s '$in_osw' 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)' &&
30 #end if 38 #end if
45 mkdir out_pout_decoy_proteins && 53 mkdir out_pout_decoy_proteins &&
46 #end if 54 #end if
47 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 55 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
48 mkdir weights && 56 mkdir weights &&
49 #end if 57 #end if
50 #if $adv_opts_cond.adv_opts_selector=='advanced': 58 #if $adv_opts.init_weights:
51 #if $adv_opts_cond.init_weights: 59 mkdir adv_opts.init_weights &&
52 mkdir adv_opts_cond.init_weights && 60 ln -s '$adv_opts.init_weights' 'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)' &&
53 ln -s '$adv_opts_cond.init_weights' 'adv_opts_cond.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts_cond.init_weights.element_identifier)}.$gxy2omsext($adv_opts_cond.init_weights.ext)' && 61 #end if
54 #end if 62 #if $adv_opts.fasta:
55 #if $adv_opts_cond.fasta: 63 mkdir adv_opts.fasta &&
56 mkdir adv_opts_cond.fasta && 64 ln -s '$adv_opts.fasta' 'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)' &&
57 ln -s '$adv_opts_cond.fasta' 'adv_opts_cond.fasta/${re.sub("[^\w\-_]", "_", $adv_opts_cond.fasta.element_identifier)}.$gxy2omsext($adv_opts_cond.fasta.ext)' && 65 #end if
58 #end if
59 #end if
60 66
61 ## Main program call 67 ## Main program call
62 68
63 set -o pipefail && 69 set -o pipefail &&
64 @EXECUTABLE@ -write_ctd ./ && 70 @EXECUTABLE@ -write_ctd ./ &&
65 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 71 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
66 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 72 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
67 #if $in: 73 #if $in_cond.in:
68 -in 74 -in
69 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 75 #if $in_cond.in_select == "no"
70 #end if 76 ${' '.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])}
71 #if $in_decoy: 77 #else
78 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
79 #end if
80 #end if
81 #if $in_decoy_cond.in_decoy:
72 -in_decoy 82 -in_decoy
73 ${' '.join(["'in_decoy/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_decoy if _])} 83 #if $in_decoy_cond.in_decoy_select == "no"
84 ${' '.join(["'in_decoy_cond.in_decoy/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_decoy_cond.in_decoy) if f])}
85 #else
86 'in_decoy_cond.in_decoy/${re.sub("[^\w\-_]", "_", $in_decoy_cond.in_decoy.element_identifier)}.$gxy2omsext($in_decoy_cond.in_decoy.ext)'
87 #end if
74 #end if 88 #end if
75 #if $in_osw: 89 #if $in_osw:
76 -in_osw 90 -in_osw
77 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)' 91 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)'
78 #end if 92 #end if
100 #end if 114 #end if
101 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 115 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
102 -weights 116 -weights
103 'weights/output.${gxy2omsext("tabular")}' 117 'weights/output.${gxy2omsext("tabular")}'
104 #end if 118 #end if
105 #if $adv_opts_cond.adv_opts_selector=='advanced': 119 #if $adv_opts.init_weights:
106 #if $adv_opts_cond.init_weights:
107 -init_weights 120 -init_weights
108 'adv_opts_cond.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts_cond.init_weights.element_identifier)}.$gxy2omsext($adv_opts_cond.init_weights.ext)' 121 'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)'
109 #end if 122 #end if
110 #if $adv_opts_cond.fasta: 123 #if $adv_opts.fasta:
111 -fasta 124 -fasta
112 'adv_opts_cond.fasta/${re.sub("[^\w\-_]", "_", $adv_opts_cond.fasta.element_identifier)}.$gxy2omsext($adv_opts_cond.fasta.ext)' 125 'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)'
113 #end if 126 #end if
114 #end if
115 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 127 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
116 | tee '$stdout' 128 | tee '$stdout'
117 #end if 129 #end if
118 130
119 ## Postprocessing 131 ## Postprocessing
142 <configfiles> 154 <configfiles>
143 <inputs name="args_json" data_style="paths"/> 155 <inputs name="args_json" data_style="paths"/>
144 <configfile name="hardcoded_json"><![CDATA[{"percolator_executable": "percolator", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 156 <configfile name="hardcoded_json"><![CDATA[{"percolator_executable": "percolator", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
145 </configfiles> 157 </configfiles>
146 <inputs> 158 <inputs>
147 <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/> 159 <conditional name="in_cond">
148 <param name="in_decoy" argument="-in_decoy" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input decoy file(s) in case of separate searches" help=" select idxml,mzid data sets(s)"/> 160 <param name="in_select" type="select" label="Run tool in batch mode for -in">
149 <param name="in_osw" argument="-in_osw" type="data" format="osw" optional="true" label="Input file in OSW format" help=" select osw data sets(s)"/> 161 <option value="no">No: process all datasets jointly</option>
150 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help=""> 162 <option value="yes">Yes: process each dataset in an independent job</option>
163 </param>
164 <when value="no">
165 <param argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
166 </when>
167 <when value="yes">
168 <param argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
169 </when>
170 </conditional>
171 <conditional name="in_decoy_cond">
172 <param name="in_decoy_select" type="select" label="Run tool in batch mode for -in_decoy">
173 <option value="no">No: process all datasets jointly</option>
174 <option value="yes">Yes: process each dataset in an independent job</option>
175 </param>
176 <when value="no">
177 <param argument="-in_decoy" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input decoy file(s) in case of separate searches" help=" select idxml,mzid data sets(s)"/>
178 </when>
179 <when value="yes">
180 <param argument="-in_decoy" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input decoy file(s) in case of separate searches" help=" select idxml,mzid data sets(s)"/>
181 </when>
182 </conditional>
183 <param argument="-in_osw" type="data" format="osw" optional="true" label="Input file in OSW format" help=" select osw data sets(s)"/>
184 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
151 <option value="idXML">idxml</option> 185 <option value="idXML">idxml</option>
152 <option value="mzid">mzid</option> 186 <option value="mzid">mzid</option>
153 <option value="osw">osw</option> 187 <option value="osw">osw</option>
154 <expand macro="list_string_san"/> 188 <expand macro="list_string_san" name="out_type"/>
155 </param> 189 </param>
156 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="Type of enzyme: no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin,trypsinp" help=""> 190 <param argument="-enzyme" type="select" optional="true" label="Type of enzyme: no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin,trypsinp" help="">
157 <option value="no_enzyme">no_enzyme</option> 191 <option value="no_enzyme">no_enzyme</option>
158 <option value="elastase">elastase</option> 192 <option value="elastase">elastase</option>
159 <option value="pepsin">pepsin</option> 193 <option value="pepsin">pepsin</option>
160 <option value="proteinasek">proteinasek</option> 194 <option value="proteinasek">proteinasek</option>
161 <option value="thermolysin">thermolysin</option> 195 <option value="thermolysin">thermolysin</option>
165 <option value="arg-c">arg-c</option> 199 <option value="arg-c">arg-c</option>
166 <option value="asp-n">asp-n</option> 200 <option value="asp-n">asp-n</option>
167 <option value="glu-c">glu-c</option> 201 <option value="glu-c">glu-c</option>
168 <option value="trypsin" selected="true">trypsin</option> 202 <option value="trypsin" selected="true">trypsin</option>
169 <option value="trypsinp">trypsinp</option> 203 <option value="trypsinp">trypsinp</option>
170 <expand macro="list_string_san"/> 204 <expand macro="list_string_san" name="enzyme"/>
171 </param> 205 </param>
172 <param name="peptide_level_fdrs" argument="-peptide_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate peptide-level FDRs instead of PSM-level FDRs" help=""/> 206 <param argument="-peptide_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate peptide-level FDRs instead of PSM-level FDRs" help=""/>
173 <param name="protein_level_fdrs" argument="-protein_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the picked protein-level FDR to infer protein probabilities" help="Use the -fasta option and -decoy_pattern to set the Fasta file and decoy pattern"/> 207 <param argument="-protein_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the picked protein-level FDR to infer protein probabilities" help="Use the -fasta option and -decoy_pattern to set the Fasta file and decoy pattern"/>
174 <param name="osw_level" argument="-osw_level" type="text" optional="true" value="ms2" label="OSW: Either &quot;ms1&quot;, &quot;ms2&quot; or &quot;transition&quot;; the data level selected for scoring" help=""> 208 <param argument="-osw_level" type="select" optional="true" label="OSW: the data level selected for scoring" help="">
175 <expand macro="list_string_san"/> 209 <option value="ms1">ms1</option>
210 <option value="ms2" selected="true">ms2</option>
211 <option value="transition">transition</option>
212 <expand macro="list_string_san" name="osw_level"/>
176 </param> 213 </param>
177 <param name="score_type" argument="-score_type" display="radio" type="select" optional="false" label="Type of the peptide main score" help=""> 214 <param argument="-score_type" type="select" optional="true" label="Type of the peptide main score" help="">
178 <option value="q-value" selected="true">q-value</option> 215 <option value="q-value" selected="true">q-value</option>
179 <option value="pep">pep</option> 216 <option value="pep">pep</option>
180 <option value="svm">svm</option> 217 <option value="svm">svm</option>
181 <expand macro="list_string_san"/> 218 <expand macro="list_string_san" name="score_type"/>
182 </param> 219 </param>
183 <expand macro="adv_opts_macro"> 220 <expand macro="adv_opts_macro">
184 <param name="generic_feature_set" argument="-generic_feature_set" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only generic" help="(i.e. not search engine specific) features. Generating search engine specific features for common search engines by PSMFeatureExtractor will typically boost the identification rate significantly"/> 221 <param argument="-generic_feature_set" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only generic" help="(i.e. not search engine specific) features. Generating search engine specific features for common search engines by PSMFeatureExtractor will typically boost the identification rate significantly"/>
185 <param name="subset_max_train" argument="-subset_max_train" type="integer" optional="true" value="0" label="Only train an SVM on a subset of &lt;x&gt; PSMs, and use the resulting score vector to evaluate the other PSMs" help="Recommended when analyzing huge numbers (&gt;1 million) of PSMs. When set to 0, all PSMs are used for training as normal"/> 222 <param argument="-subset_max_train" type="integer" optional="true" value="0" label="Only train an SVM on a subset of &lt;x&gt; PSMs, and use the resulting score vector to evaluate the other PSMs" help="Recommended when analyzing huge numbers (&gt;1 million) of PSMs. When set to 0, all PSMs are used for training as normal"/>
186 <param name="cpos" argument="-cpos" type="float" optional="true" value="0.0" label="Cpos, penalty for mistakes made on positive examples" help="Set by cross validation if not specified"/> 223 <param argument="-cpos" type="float" optional="true" value="0.0" label="Cpos, penalty for mistakes made on positive examples" help="Set by cross validation if not specified"/>
187 <param name="cneg" argument="-cneg" type="float" optional="true" value="0.0" label="Cneg, penalty for mistakes made on negative examples" help="Set by cross validation if not specified"/> 224 <param argument="-cneg" type="float" optional="true" value="0.0" label="Cneg, penalty for mistakes made on negative examples" help="Set by cross validation if not specified"/>
188 <param name="testFDR" argument="-testFDR" type="float" optional="true" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help=""/> 225 <param argument="-testFDR" type="float" optional="true" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help=""/>
189 <param name="trainFDR" argument="-trainFDR" type="float" optional="true" value="0.01" label="False discovery rate threshold to define positive examples in training" help="Set to testFDR if 0"/> 226 <param argument="-trainFDR" type="float" optional="true" value="0.01" label="False discovery rate threshold to define positive examples in training" help="Set to testFDR if 0"/>
190 <param name="maxiter" argument="-maxiter" type="integer" optional="true" value="10" label="Maximal number of iterations" help=""/> 227 <param argument="-maxiter" type="integer" optional="true" value="10" label="Maximal number of iterations" help=""/>
191 <param name="nested_xval_bins" argument="-nested_xval_bins" type="integer" optional="true" value="1" label="Number of nested cross-validation bins in the 3 splits" help=""/> 228 <param argument="-nested_xval_bins" type="integer" optional="true" value="1" label="Number of nested cross-validation bins in the 3 splits" help=""/>
192 <param name="quick_validation" argument="-quick_validation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Quicker execution by reduced internal cross-validation" help=""/> 229 <param argument="-quick_validation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Quicker execution by reduced internal cross-validation" help=""/>
193 <param name="init_weights" argument="-init_weights" type="data" format="tabular" optional="true" label="Read initial weights to the given file" help=" select tabular data sets(s)"/> 230 <param argument="-init_weights" type="data" format="tabular" optional="true" label="Read initial weights to the given file" help=" select tabular data sets(s)"/>
194 <param name="static" argument="-static" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use static model (requires init-weights parameter to be set)" help=""/> 231 <param argument="-static" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use static model (requires init-weights parameter to be set)" help=""/>
195 <param name="default_direction" argument="-default_direction" type="text" optional="true" value="" label="The most informative feature given as the feature name, can be negated to indicate that a lower value is bette" help=""> 232 <param argument="-default_direction" type="text" optional="true" value="" label="The most informative feature given as the feature name, can be negated to indicate that a lower value is bette" help="">
196 <expand macro="list_string_san"/> 233 <expand macro="list_string_san" name="default_direction"/>
197 </param> 234 </param>
198 <param name="verbose" argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/> 235 <param argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/>
199 <param name="unitnorm" argument="-unitnorm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use unit normalization [0-1] instead of standard deviation normalization" help=""/> 236 <param argument="-unitnorm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use unit normalization [0-1] instead of standard deviation normalization" help=""/>
200 <param name="test_each_iteration" argument="-test_each_iteration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Measure performance on test set each iteration" help=""/> 237 <param argument="-test_each_iteration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Measure performance on test set each iteration" help=""/>
201 <param name="override" argument="-override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override error check and do not fall back on default score vector in case of suspect score vecto" help=""/> 238 <param argument="-override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override error check and do not fall back on default score vector in case of suspect score vecto" help=""/>
202 <param name="seed" argument="-seed" type="integer" optional="true" value="1" label="Setting seed of the random number generato" help=""/> 239 <param argument="-seed" type="integer" optional="true" value="1" label="Setting seed of the random number generato" help=""/>
203 <param name="doc" argument="-doc" type="integer" optional="true" value="0" label="Include description of correct features" help=""/> 240 <param argument="-doc" type="integer" optional="true" value="0" label="Include description of correct features" help=""/>
204 <param name="klammer" argument="-klammer" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Retention time features calculated as in Klammer et al" help="Only available if -doc is set"/> 241 <param argument="-klammer" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Retention time features calculated as in Klammer et al" help="Only available if -doc is set"/>
205 <param name="fasta" argument="-fasta" type="data" format="fasta" optional="true" label="Provide the fasta file as the argument to this flag, which will be used for protein grouping based on an in-silico digest (only valid if option -protein_level_fdrs is active)" help=" select fasta data sets(s)"/> 242 <param argument="-fasta" type="data" format="fasta" optional="true" label="Provide the fasta file as the argument to this flag, which will be used for protein grouping based on an in-silico digest (only valid if option -protein_level_fdrs is active)" help=" select fasta data sets(s)"/>
206 <param name="decoy_pattern" argument="-decoy_pattern" type="text" optional="true" value="random" label="Define the text pattern to identify the decoy proteins and/or PSMs, set this up if the label that identifies the decoys in the database is not the default (Only valid if option -protein_level_fdrs is active)" help=""> 243 <param argument="-decoy_pattern" type="text" optional="true" value="random" label="Define the text pattern to identify the decoy proteins and/or PSMs, set this up if the label that identifies the decoys in the database is not the default (Only valid if option -protein_level_fdrs is active)" help="">
207 <expand macro="list_string_san"/> 244 <expand macro="list_string_san" name="decoy_pattern"/>
208 </param> 245 </param>
209 <param name="post_processing_tdc" argument="-post_processing_tdc" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use target-decoy competition to assign q-values and PEPs" help=""/> 246 <param argument="-post_processing_tdc" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use target-decoy competition to assign q-values and PEPs" help=""/>
210 <param name="train_best_positive" argument="-train_best_positive" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enforce that, for each spectrum, at most one PSM is included in the positive set during each training iteration" help="If the user only provides one PSM per spectrum, this filter will have no effect"/> 247 <param argument="-train_best_positive" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enforce that, for each spectrum, at most one PSM is included in the positive set during each training iteration" help="If the user only provides one PSM per spectrum, this filter will have no effect"/>
211 <param name="ipf_max_peakgroup_pep" argument="-ipf_max_peakgroup_pep" type="float" optional="true" value="0.7" label="OSW/IPF: Assess transitions only for candidate peak groups until maximum posterior error probability" help=""/> 248 <param argument="-ipf_max_peakgroup_pep" type="float" optional="true" value="0.7" label="OSW/IPF: Assess transitions only for candidate peak groups until maximum posterior error probability" help=""/>
212 <param name="ipf_max_transition_isotope_overlap" argument="-ipf_max_transition_isotope_overlap" type="float" optional="true" value="0.5" label="OSW/IPF: Maximum isotope overlap to consider transitions in IPF" help=""/> 249 <param argument="-ipf_max_transition_isotope_overlap" type="float" optional="true" value="0.5" label="OSW/IPF: Maximum isotope overlap to consider transitions in IPF" help=""/>
213 <param name="ipf_min_transition_sn" argument="-ipf_min_transition_sn" type="float" optional="true" value="0.0" label="OSW/IPF: Minimum log signal-to-noise level to consider transitions in IPF" help="Set -1 to disable this filter"/> 250 <param argument="-ipf_min_transition_sn" type="float" optional="true" value="0.0" label="OSW/IPF: Minimum log signal-to-noise level to consider transitions in IPF" help="Set -1 to disable this filter"/>
214 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 251 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
215 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 252 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
216 <expand macro="list_string_san"/> 253 <expand macro="list_string_san" name="test"/>
217 </param> 254 </param>
218 </expand> 255 </expand>
219 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 256 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
220 <option value="out_pin_FLAG">out_pin (Write pin file (e.g., for debugging))</option> 257 <option value="out_pin_FLAG">out_pin (Write pin file (e.g., for debugging))</option>
221 <option value="out_pout_target_FLAG">out_pout_target (Write pout file (e.g., for debugging))</option> 258 <option value="out_pout_target_FLAG">out_pout_target (Write pout file (e.g., for debugging))</option>
225 <option value="weights_FLAG">weights (Output final weights to the given file)</option> 262 <option value="weights_FLAG">weights (Output final weights to the given file)</option>
226 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 263 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
227 </param> 264 </param>
228 </inputs> 265 </inputs>
229 <outputs> 266 <outputs>
230 <data name="out" label="${tool.name} on ${on_string}: out"> 267 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
231 <change_format> 268 <change_format>
232 <when input="out_type" value="idXML" format="idxml"/>
233 <when input="out_type" value="mzid" format="mzid"/> 269 <when input="out_type" value="mzid" format="mzid"/>
234 <when input="out_type" value="osw" format="osw"/> 270 <when input="out_type" value="osw" format="osw"/>
235 </change_format> 271 </change_format>
236 </data> 272 </data>
237 <data name="out_pin" label="${tool.name} on ${on_string}: out_pin" format="tabular"> 273 <data name="out_pin" label="${tool.name} on ${on_string}: out_pin" format="tabular">
254 </data> 290 </data>
255 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 291 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
256 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 292 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
257 </data> 293 </data>
258 </outputs> 294 </outputs>
259 <tests> 295 <tests><!-- TOPP_PercolatorAdapter_1 -->
260 <expand macro="autotest_PercolatorAdapter"/> 296 <test expect_num_outputs="2">
261 <expand macro="manutest_PercolatorAdapter"/> 297 <section name="adv_opts">
298 <param name="generic_feature_set" value="false"/>
299 <param name="subset_max_train" value="0"/>
300 <param name="cpos" value="0.0"/>
301 <param name="cneg" value="0.0"/>
302 <param name="testFDR" value="0.5"/>
303 <param name="trainFDR" value="0.5"/>
304 <param name="maxiter" value="10"/>
305 <param name="nested_xval_bins" value="1"/>
306 <param name="quick_validation" value="false"/>
307 <param name="static" value="false"/>
308 <param name="default_direction" value=""/>
309 <param name="verbose" value="2"/>
310 <param name="unitnorm" value="false"/>
311 <param name="test_each_iteration" value="false"/>
312 <param name="override" value="false"/>
313 <param name="seed" value="1"/>
314 <param name="doc" value="0"/>
315 <param name="klammer" value="false"/>
316 <param name="decoy_pattern" value="random"/>
317 <param name="post_processing_tdc" value="false"/>
318 <param name="train_best_positive" value="false"/>
319 <param name="ipf_max_peakgroup_pep" value="0.7"/>
320 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
321 <param name="ipf_min_transition_sn" value="0.0"/>
322 <param name="force" value="false"/>
323 <param name="test" value="true"/>
324 </section>
325 <conditional name="in_cond">
326 <param name="in" value="PercolatorAdapter_1.idXML"/>
327 </conditional>
328 <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
329 <param name="out_type" value="idXML"/>
330 <param name="enzyme" value="trypsin"/>
331 <param name="peptide_level_fdrs" value="false"/>
332 <param name="protein_level_fdrs" value="false"/>
333 <param name="osw_level" value="ms2"/>
334 <param name="score_type" value="q-value"/>
335 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
336 <output name="ctd_out" ftype="xml">
337 <assert_contents>
338 <is_valid_xml/>
339 </assert_contents>
340 </output>
341 </test>
342 <!-- TOPP_PercolatorAdapter_2 -->
343 <test expect_num_outputs="2">
344 <section name="adv_opts">
345 <param name="generic_feature_set" value="false"/>
346 <param name="subset_max_train" value="0"/>
347 <param name="cpos" value="0.0"/>
348 <param name="cneg" value="0.0"/>
349 <param name="testFDR" value="0.01"/>
350 <param name="trainFDR" value="0.01"/>
351 <param name="maxiter" value="10"/>
352 <param name="nested_xval_bins" value="1"/>
353 <param name="quick_validation" value="false"/>
354 <param name="static" value="false"/>
355 <param name="default_direction" value=""/>
356 <param name="verbose" value="2"/>
357 <param name="unitnorm" value="false"/>
358 <param name="test_each_iteration" value="false"/>
359 <param name="override" value="false"/>
360 <param name="seed" value="1"/>
361 <param name="doc" value="0"/>
362 <param name="klammer" value="false"/>
363 <param name="decoy_pattern" value="random"/>
364 <param name="post_processing_tdc" value="false"/>
365 <param name="train_best_positive" value="false"/>
366 <param name="ipf_max_peakgroup_pep" value="0.7"/>
367 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
368 <param name="ipf_min_transition_sn" value="0.0"/>
369 <param name="force" value="false"/>
370 <param name="test" value="true"/>
371 </section>
372 <param name="in_osw" value="PercolatorAdapter_2.osw"/>
373 <output name="out" file="PercolatorAdapter_2_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
374 <param name="out_type" value="osw"/>
375 <param name="enzyme" value="trypsin"/>
376 <param name="peptide_level_fdrs" value="false"/>
377 <param name="protein_level_fdrs" value="false"/>
378 <param name="osw_level" value="ms1"/>
379 <param name="score_type" value="q-value"/>
380 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
381 <output name="ctd_out" ftype="xml">
382 <assert_contents>
383 <is_valid_xml/>
384 </assert_contents>
385 </output>
386 </test>
387 <!-- TOPP_PercolatorAdapter_3 -->
388 <test expect_num_outputs="2">
389 <section name="adv_opts">
390 <param name="generic_feature_set" value="false"/>
391 <param name="subset_max_train" value="0"/>
392 <param name="cpos" value="0.0"/>
393 <param name="cneg" value="0.0"/>
394 <param name="testFDR" value="0.01"/>
395 <param name="trainFDR" value="0.01"/>
396 <param name="maxiter" value="10"/>
397 <param name="nested_xval_bins" value="1"/>
398 <param name="quick_validation" value="false"/>
399 <param name="static" value="false"/>
400 <param name="default_direction" value=""/>
401 <param name="verbose" value="2"/>
402 <param name="unitnorm" value="false"/>
403 <param name="test_each_iteration" value="false"/>
404 <param name="override" value="false"/>
405 <param name="seed" value="1"/>
406 <param name="doc" value="0"/>
407 <param name="klammer" value="false"/>
408 <param name="decoy_pattern" value="random"/>
409 <param name="post_processing_tdc" value="false"/>
410 <param name="train_best_positive" value="false"/>
411 <param name="ipf_max_peakgroup_pep" value="0.7"/>
412 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
413 <param name="ipf_min_transition_sn" value="0.0"/>
414 <param name="force" value="false"/>
415 <param name="test" value="true"/>
416 </section>
417 <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/>
418 <output name="out" file="PercolatorAdapter_3_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
419 <param name="out_type" value="osw"/>
420 <param name="enzyme" value="trypsin"/>
421 <param name="peptide_level_fdrs" value="false"/>
422 <param name="protein_level_fdrs" value="false"/>
423 <param name="osw_level" value="ms2"/>
424 <param name="score_type" value="q-value"/>
425 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
426 <output name="ctd_out" ftype="xml">
427 <assert_contents>
428 <is_valid_xml/>
429 </assert_contents>
430 </output>
431 </test>
432 <!-- TOPP_PercolatorAdapter_4 -->
433 <test expect_num_outputs="2">
434 <section name="adv_opts">
435 <param name="generic_feature_set" value="false"/>
436 <param name="subset_max_train" value="0"/>
437 <param name="cpos" value="0.0"/>
438 <param name="cneg" value="0.0"/>
439 <param name="testFDR" value="0.01"/>
440 <param name="trainFDR" value="0.01"/>
441 <param name="maxiter" value="10"/>
442 <param name="nested_xval_bins" value="1"/>
443 <param name="quick_validation" value="false"/>
444 <param name="static" value="false"/>
445 <param name="default_direction" value=""/>
446 <param name="verbose" value="2"/>
447 <param name="unitnorm" value="false"/>
448 <param name="test_each_iteration" value="false"/>
449 <param name="override" value="false"/>
450 <param name="seed" value="1"/>
451 <param name="doc" value="0"/>
452 <param name="klammer" value="false"/>
453 <param name="decoy_pattern" value="random"/>
454 <param name="post_processing_tdc" value="false"/>
455 <param name="train_best_positive" value="false"/>
456 <param name="ipf_max_peakgroup_pep" value="0.7"/>
457 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
458 <param name="ipf_min_transition_sn" value="0.0"/>
459 <param name="force" value="false"/>
460 <param name="test" value="true"/>
461 </section>
462 <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/>
463 <output name="out" file="PercolatorAdapter_4_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
464 <param name="out_type" value="osw"/>
465 <param name="enzyme" value="trypsin"/>
466 <param name="peptide_level_fdrs" value="false"/>
467 <param name="protein_level_fdrs" value="false"/>
468 <param name="osw_level" value="transition"/>
469 <param name="score_type" value="q-value"/>
470 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
471 <output name="ctd_out" ftype="xml">
472 <assert_contents>
473 <is_valid_xml/>
474 </assert_contents>
475 </output>
476 </test>
477 <!-- TOPP_PercolatorAdapter_5 -->
478 <test expect_num_outputs="3">
479 <section name="adv_opts">
480 <param name="generic_feature_set" value="false"/>
481 <param name="subset_max_train" value="0"/>
482 <param name="cpos" value="0.0"/>
483 <param name="cneg" value="0.0"/>
484 <param name="testFDR" value="0.5"/>
485 <param name="trainFDR" value="0.5"/>
486 <param name="maxiter" value="10"/>
487 <param name="nested_xval_bins" value="1"/>
488 <param name="quick_validation" value="false"/>
489 <param name="static" value="false"/>
490 <param name="default_direction" value=""/>
491 <param name="verbose" value="2"/>
492 <param name="unitnorm" value="false"/>
493 <param name="test_each_iteration" value="false"/>
494 <param name="override" value="false"/>
495 <param name="seed" value="1"/>
496 <param name="doc" value="0"/>
497 <param name="klammer" value="false"/>
498 <param name="decoy_pattern" value="random"/>
499 <param name="post_processing_tdc" value="false"/>
500 <param name="train_best_positive" value="false"/>
501 <param name="ipf_max_peakgroup_pep" value="0.7"/>
502 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
503 <param name="ipf_min_transition_sn" value="0.0"/>
504 <param name="force" value="false"/>
505 <param name="test" value="true"/>
506 </section>
507 <conditional name="in_cond">
508 <param name="in" value="PercolatorAdapter_1.idXML"/>
509 </conditional>
510 <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
511 <output name="out_pin" file="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
512 <param name="out_type" value="idXML"/>
513 <param name="enzyme" value="trypsin"/>
514 <param name="peptide_level_fdrs" value="false"/>
515 <param name="protein_level_fdrs" value="false"/>
516 <param name="osw_level" value="ms2"/>
517 <param name="score_type" value="q-value"/>
518 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pin_FLAG"/>
519 <output name="ctd_out" ftype="xml">
520 <assert_contents>
521 <is_valid_xml/>
522 </assert_contents>
523 </output>
524 </test>
262 </tests> 525 </tests>
263 <help><![CDATA[Facilitate input to Percolator and reintegrate. 526 <help><![CDATA[Facilitate input to Percolator and reintegrate.
264 527
265 528
266 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PercolatorAdapter.html]]></help> 529 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PercolatorAdapter.html]]></help>
267 <expand macro="references"/> 530 <expand macro="references"/>
268 </tool> 531 </tool>