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comparison PercolatorAdapter.xml @ 9:02796e3ddec1 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 21:34:28 +0000
parents 016964c597f5
children
comparison
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8:016964c597f5 9:02796e3ddec1
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Identification Processing]-->
4 <tool id="PercolatorAdapter" name="PercolatorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="PercolatorAdapter" name="PercolatorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Facilitate input to Percolator and reintegrate.</description> 4 <description>Facilitate input to Percolator and reintegrate</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">PercolatorAdapter</token> 6 <token name="@EXECUTABLE@">PercolatorAdapter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
16 ## Preprocessing 15 ## Preprocessing
17 #if $in_cond.in: 16 #if $in_cond.in:
18 mkdir in_cond.in && 17 mkdir in_cond.in &&
19 #if $in_cond.in_select == "no" 18 #if $in_cond.in_select == "no"
20 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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])} 20 ${' '.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])}
22 #else 21 #else
23 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && 22 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
24 #end if 23 #end if
25 #end if 24 #end if
26 #if $in_decoy_cond.in_decoy: 25 #if $in_decoy_cond.in_decoy:
27 mkdir in_decoy_cond.in_decoy && 26 mkdir in_decoy_cond.in_decoy &&
28 #if $in_decoy_cond.in_decoy_select == "no" 27 #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])} && 28 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])} 29 ${' '.join(["cp '%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 30 #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($in_decoy_cond.in_decoy.ext)' && 31 cp '$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 32 #end if
34 #end if 33 #end if
35 #if $in_osw: 34 #if $in_osw:
36 mkdir in_osw && 35 mkdir in_osw &&
37 ln -s '$in_osw' 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)' && 36 cp '$in_osw' 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)' &&
38 #end if 37 #end if
39 mkdir out && 38 mkdir out &&
40 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 39 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
41 mkdir out_pin && 40 mkdir out_pin &&
42 #end if 41 #end if
53 mkdir out_pout_decoy_proteins && 52 mkdir out_pout_decoy_proteins &&
54 #end if 53 #end if
55 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 54 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
56 mkdir weights && 55 mkdir weights &&
57 #end if 56 #end if
57 ## advanced options
58 #if $adv_opts.init_weights: 58 #if $adv_opts.init_weights:
59 mkdir adv_opts.init_weights && 59 mkdir adv_opts.init_weights &&
60 ln -s '$adv_opts.init_weights' 'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)' && 60 cp '$adv_opts.init_weights' 'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)' &&
61 #end if 61 #end if
62 #if $adv_opts.fasta: 62 #if $adv_opts.fasta:
63 mkdir adv_opts.fasta && 63 mkdir adv_opts.fasta &&
64 ln -s '$adv_opts.fasta' 'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)' && 64 cp '$adv_opts.fasta' 'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)' &&
65 #end if 65 #end if
66
66 67
67 ## Main program call 68 ## Main program call
68 69
69 set -o pipefail && 70 set -o pipefail &&
70 @EXECUTABLE@ -write_ctd ./ && 71 @EXECUTABLE@ -write_ctd ./ &&
114 #end if 115 #end if
115 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 116 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
116 -weights 117 -weights
117 'weights/output.${gxy2omsext("tabular")}' 118 'weights/output.${gxy2omsext("tabular")}'
118 #end if 119 #end if
120 ## advanced options
119 #if $adv_opts.init_weights: 121 #if $adv_opts.init_weights:
120 -init_weights 122 -init_weights
121 'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)' 123 'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)'
122 #end if 124 #end if
123 #if $adv_opts.fasta: 125 #if $adv_opts.fasta:
124 -fasta 126 -fasta
125 'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)' 127 'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)'
126 #end if 128 #end if
129
127 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 130 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
128 | tee '$stdout' 131 | tee '$stdout'
129 #end if 132 #end if
130 133
131 ## Postprocessing 134 ## Postprocessing
163 </param> 166 </param>
164 <when value="no"> 167 <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)"/> 168 <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> 169 </when>
167 <when value="yes"> 170 <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)"/> 171 <param argument="-in" type="data" format="idxml,mzid" optional="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
169 </when> 172 </when>
170 </conditional> 173 </conditional>
171 <conditional name="in_decoy_cond"> 174 <conditional name="in_decoy_cond">
172 <param name="in_decoy_select" type="select" label="Run tool in batch mode for -in_decoy"> 175 <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> 176 <option value="no">No: process all datasets jointly</option>
175 </param> 178 </param>
176 <when value="no"> 179 <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)"/> 180 <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> 181 </when>
179 <when value="yes"> 182 <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)"/> 183 <param argument="-in_decoy" type="data" format="idxml,mzid" optional="true" label="Input decoy file(s) in case of separate searches" help=" select idxml,mzid data sets(s)"/>
181 </when> 184 </when>
182 </conditional> 185 </conditional>
183 <param argument="-in_osw" type="data" format="osw" optional="true" label="Input file in OSW format" help=" select osw data sets(s)"/> 186 <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=""> 187 <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
185 <option value="idXML">idxml</option> 188 <option value="idXML">idxml</option>
186 <option value="mzid">mzid</option> 189 <option value="mzid">mzid</option>
187 <option value="osw">osw</option> 190 <option value="osw">osw</option>
191 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
188 <expand macro="list_string_san" name="out_type"/> 192 <expand macro="list_string_san" name="out_type"/>
189 </param> 193 </param>
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=""> 194 <param argument="-enzyme" type="select" label="Type of enzyme: no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin,trypsinp" help="">
191 <option value="no_enzyme">no_enzyme</option> 195 <option value="no_enzyme">no_enzyme</option>
192 <option value="elastase">elastase</option> 196 <option value="elastase">elastase</option>
193 <option value="pepsin">pepsin</option> 197 <option value="pepsin">pepsin</option>
194 <option value="proteinasek">proteinasek</option> 198 <option value="proteinasek">proteinasek</option>
195 <option value="thermolysin">thermolysin</option> 199 <option value="thermolysin">thermolysin</option>
203 <option value="trypsinp">trypsinp</option> 207 <option value="trypsinp">trypsinp</option>
204 <expand macro="list_string_san" name="enzyme"/> 208 <expand macro="list_string_san" name="enzyme"/>
205 </param> 209 </param>
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=""/> 210 <param argument="-peptide_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate peptide-level FDRs instead of PSM-level FDRs" help=""/>
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"/> 211 <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"/>
208 <param argument="-osw_level" type="select" optional="true" label="OSW: the data level selected for scoring" help=""> 212 <param argument="-osw_level" type="select" label="OSW: the data level selected for scoring" help="">
209 <option value="ms1">ms1</option> 213 <option value="ms1">ms1</option>
210 <option value="ms2" selected="true">ms2</option> 214 <option value="ms2" selected="true">ms2</option>
211 <option value="transition">transition</option> 215 <option value="transition">transition</option>
212 <expand macro="list_string_san" name="osw_level"/> 216 <expand macro="list_string_san" name="osw_level"/>
213 </param> 217 </param>
214 <param argument="-score_type" type="select" optional="true" label="Type of the peptide main score" help=""> 218 <param argument="-score_type" type="select" label="Type of the peptide main score" help="">
215 <option value="q-value" selected="true">q-value</option> 219 <option value="q-value" selected="true">q-value</option>
216 <option value="pep">pep</option> 220 <option value="pep">pep</option>
217 <option value="svm">svm</option> 221 <option value="svm">svm</option>
218 <expand macro="list_string_san" name="score_type"/> 222 <expand macro="list_string_san" name="score_type"/>
219 </param> 223 </param>
220 <expand macro="adv_opts_macro"> 224 <expand macro="adv_opts_macro">
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"/> 225 <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"/>
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"/> 226 <param argument="-subset_max_train" type="integer" 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"/>
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"/> 227 <param argument="-cpos" type="float" value="0.0" label="Cpos, penalty for mistakes made on positive 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"/> 228 <param argument="-cneg" type="float" value="0.0" label="Cneg, penalty for mistakes made on negative examples" help="Set by cross validation if not specified"/>
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=""/> 229 <param argument="-testFDR" type="float" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help=""/>
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"/> 230 <param argument="-trainFDR" type="float" value="0.01" label="False discovery rate threshold to define positive examples in training" help="Set to testFDR if 0"/>
227 <param argument="-maxiter" type="integer" optional="true" value="10" label="Maximal number of iterations" help=""/> 231 <param argument="-maxiter" type="integer" value="10" label="Maximal number of iterations" 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=""/> 232 <param argument="-nested_xval_bins" type="integer" value="1" label="Number of nested cross-validation bins in the 3 splits" help=""/>
229 <param argument="-quick_validation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Quicker execution by reduced internal cross-validation" help=""/> 233 <param argument="-quick_validation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Quicker execution by reduced internal cross-validation" help=""/>
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)"/> 234 <param argument="-init_weights" type="data" format="tabular" optional="true" label="Read initial weights to the given file" help=" select tabular data sets(s)"/>
231 <param argument="-static" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use static model (requires init-weights parameter to be set)" help=""/> 235 <param argument="-static" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use static model (requires init-weights parameter to be set)" 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=""> 236 <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="">
233 <expand macro="list_string_san" name="default_direction"/> 237 <expand macro="list_string_san" name="default_direction"/>
234 </param> 238 </param>
235 <param argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/> 239 <param argument="-verbose" type="integer" value="2" label="Set verbosity of output: 0=no processing info, 5=all" 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=""/> 240 <param argument="-unitnorm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use unit normalization [0-1] instead of standard deviation normalization" help=""/>
237 <param argument="-test_each_iteration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Measure performance on test set each iteration" help=""/> 241 <param argument="-test_each_iteration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Measure performance on test set each iteration" 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=""/> 242 <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=""/>
239 <param argument="-seed" type="integer" optional="true" value="1" label="Setting seed of the random number generato" help=""/> 243 <param argument="-seed" type="integer" value="1" label="Setting seed of the random number generato" help=""/>
240 <param argument="-doc" type="integer" optional="true" value="0" label="Include description of correct features" help=""/> 244 <param argument="-doc" type="integer" value="0" label="Include description of correct features" help=""/>
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"/> 245 <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"/>
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)"/> 246 <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)"/>
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=""> 247 <param argument="-decoy_pattern" type="text" 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="">
244 <expand macro="list_string_san" name="decoy_pattern"/> 248 <expand macro="list_string_san" name="decoy_pattern"/>
245 </param> 249 </param>
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=""/> 250 <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=""/>
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"/> 251 <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"/>
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=""/> 252 <param argument="-ipf_max_peakgroup_pep" type="float" value="0.7" label="OSW/IPF: Assess transitions only for candidate peak groups until maximum posterior error probability" 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=""/> 253 <param argument="-ipf_max_transition_isotope_overlap" type="float" value="0.5" label="OSW/IPF: Maximum isotope overlap to consider transitions in IPF" help=""/>
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"/> 254 <param argument="-ipf_min_transition_sn" type="float" value="0.0" label="OSW/IPF: Minimum log signal-to-noise level to consider transitions in IPF" help="Set -1 to disable this filter"/>
251 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 255 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
252 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 256 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
253 <expand macro="list_string_san" name="test"/> 257 <expand macro="list_string_san" name="test"/>
254 </param> 258 </param>
255 </expand> 259 </expand>
256 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 260 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
257 <option value="out_pin_FLAG">out_pin (Write pin file (e.g., for debugging))</option> 261 <option value="out_pin_FLAG">out_pin (Write pin file (e.g., for debugging))</option>
290 </data> 294 </data>
291 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 295 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
292 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 296 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
293 </data> 297 </data>
294 </outputs> 298 </outputs>
295 <tests><!-- TOPP_PercolatorAdapter_1 --> 299 <tests>
300 <!-- TOPP_PercolatorAdapter_1 -->
296 <test expect_num_outputs="2"> 301 <test expect_num_outputs="2">
297 <section name="adv_opts"> 302 <section name="adv_opts">
298 <param name="generic_feature_set" value="false"/> 303 <param name="generic_feature_set" value="false"/>
299 <param name="subset_max_train" value="0"/> 304 <param name="subset_max_train" value="0"/>
300 <param name="cpos" value="0.0"/> 305 <param name="cpos" value="0.0"/>
323 <param name="test" value="true"/> 328 <param name="test" value="true"/>
324 </section> 329 </section>
325 <conditional name="in_cond"> 330 <conditional name="in_cond">
326 <param name="in" value="PercolatorAdapter_1.idXML"/> 331 <param name="in" value="PercolatorAdapter_1.idXML"/>
327 </conditional> 332 </conditional>
328 <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 333 <output name="out" value="PercolatorAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
329 <param name="out_type" value="idXML"/> 334 <param name="out_type" value="idXML"/>
330 <param name="enzyme" value="trypsin"/> 335 <param name="enzyme" value="trypsin"/>
331 <param name="peptide_level_fdrs" value="false"/> 336 <param name="peptide_level_fdrs" value="false"/>
332 <param name="protein_level_fdrs" value="false"/> 337 <param name="protein_level_fdrs" value="false"/>
333 <param name="osw_level" value="ms2"/> 338 <param name="osw_level" value="ms2"/>
336 <output name="ctd_out" ftype="xml"> 341 <output name="ctd_out" ftype="xml">
337 <assert_contents> 342 <assert_contents>
338 <is_valid_xml/> 343 <is_valid_xml/>
339 </assert_contents> 344 </assert_contents>
340 </output> 345 </output>
346 <assert_stdout>
347 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
348 </assert_stdout>
341 </test> 349 </test>
342 <!-- TOPP_PercolatorAdapter_2 --> 350 <!-- TOPP_PercolatorAdapter_2 -->
343 <test expect_num_outputs="2"> 351 <test expect_num_outputs="2">
344 <section name="adv_opts"> 352 <section name="adv_opts">
345 <param name="generic_feature_set" value="false"/> 353 <param name="generic_feature_set" value="false"/>
368 <param name="ipf_min_transition_sn" value="0.0"/> 376 <param name="ipf_min_transition_sn" value="0.0"/>
369 <param name="force" value="false"/> 377 <param name="force" value="false"/>
370 <param name="test" value="true"/> 378 <param name="test" value="true"/>
371 </section> 379 </section>
372 <param name="in_osw" value="PercolatorAdapter_2.osw"/> 380 <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"/> 381 <output name="out" value="PercolatorAdapter_2_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
374 <param name="out_type" value="osw"/> 382 <param name="out_type" value="osw"/>
375 <param name="enzyme" value="trypsin"/> 383 <param name="enzyme" value="trypsin"/>
376 <param name="peptide_level_fdrs" value="false"/> 384 <param name="peptide_level_fdrs" value="false"/>
377 <param name="protein_level_fdrs" value="false"/> 385 <param name="protein_level_fdrs" value="false"/>
378 <param name="osw_level" value="ms1"/> 386 <param name="osw_level" value="ms1"/>
381 <output name="ctd_out" ftype="xml"> 389 <output name="ctd_out" ftype="xml">
382 <assert_contents> 390 <assert_contents>
383 <is_valid_xml/> 391 <is_valid_xml/>
384 </assert_contents> 392 </assert_contents>
385 </output> 393 </output>
394 <assert_stdout>
395 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
396 </assert_stdout>
386 </test> 397 </test>
387 <!-- TOPP_PercolatorAdapter_3 --> 398 <!-- TOPP_PercolatorAdapter_3 -->
388 <test expect_num_outputs="2"> 399 <test expect_num_outputs="2">
389 <section name="adv_opts"> 400 <section name="adv_opts">
390 <param name="generic_feature_set" value="false"/> 401 <param name="generic_feature_set" value="false"/>
413 <param name="ipf_min_transition_sn" value="0.0"/> 424 <param name="ipf_min_transition_sn" value="0.0"/>
414 <param name="force" value="false"/> 425 <param name="force" value="false"/>
415 <param name="test" value="true"/> 426 <param name="test" value="true"/>
416 </section> 427 </section>
417 <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/> 428 <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"/> 429 <output name="out" value="PercolatorAdapter_3_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
419 <param name="out_type" value="osw"/> 430 <param name="out_type" value="osw"/>
420 <param name="enzyme" value="trypsin"/> 431 <param name="enzyme" value="trypsin"/>
421 <param name="peptide_level_fdrs" value="false"/> 432 <param name="peptide_level_fdrs" value="false"/>
422 <param name="protein_level_fdrs" value="false"/> 433 <param name="protein_level_fdrs" value="false"/>
423 <param name="osw_level" value="ms2"/> 434 <param name="osw_level" value="ms2"/>
426 <output name="ctd_out" ftype="xml"> 437 <output name="ctd_out" ftype="xml">
427 <assert_contents> 438 <assert_contents>
428 <is_valid_xml/> 439 <is_valid_xml/>
429 </assert_contents> 440 </assert_contents>
430 </output> 441 </output>
442 <assert_stdout>
443 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
444 </assert_stdout>
431 </test> 445 </test>
432 <!-- TOPP_PercolatorAdapter_4 --> 446 <!-- TOPP_PercolatorAdapter_4 -->
433 <test expect_num_outputs="2"> 447 <test expect_num_outputs="2">
434 <section name="adv_opts"> 448 <section name="adv_opts">
435 <param name="generic_feature_set" value="false"/> 449 <param name="generic_feature_set" value="false"/>
458 <param name="ipf_min_transition_sn" value="0.0"/> 472 <param name="ipf_min_transition_sn" value="0.0"/>
459 <param name="force" value="false"/> 473 <param name="force" value="false"/>
460 <param name="test" value="true"/> 474 <param name="test" value="true"/>
461 </section> 475 </section>
462 <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/> 476 <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"/> 477 <output name="out" value="PercolatorAdapter_4_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
464 <param name="out_type" value="osw"/> 478 <param name="out_type" value="osw"/>
465 <param name="enzyme" value="trypsin"/> 479 <param name="enzyme" value="trypsin"/>
466 <param name="peptide_level_fdrs" value="false"/> 480 <param name="peptide_level_fdrs" value="false"/>
467 <param name="protein_level_fdrs" value="false"/> 481 <param name="protein_level_fdrs" value="false"/>
468 <param name="osw_level" value="transition"/> 482 <param name="osw_level" value="transition"/>
471 <output name="ctd_out" ftype="xml"> 485 <output name="ctd_out" ftype="xml">
472 <assert_contents> 486 <assert_contents>
473 <is_valid_xml/> 487 <is_valid_xml/>
474 </assert_contents> 488 </assert_contents>
475 </output> 489 </output>
490 <assert_stdout>
491 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
492 </assert_stdout>
476 </test> 493 </test>
477 <!-- TOPP_PercolatorAdapter_5 --> 494 <!-- TOPP_PercolatorAdapter_5 -->
478 <test expect_num_outputs="3"> 495 <test expect_num_outputs="3">
479 <section name="adv_opts"> 496 <section name="adv_opts">
480 <param name="generic_feature_set" value="false"/> 497 <param name="generic_feature_set" value="false"/>
505 <param name="test" value="true"/> 522 <param name="test" value="true"/>
506 </section> 523 </section>
507 <conditional name="in_cond"> 524 <conditional name="in_cond">
508 <param name="in" value="PercolatorAdapter_1.idXML"/> 525 <param name="in" value="PercolatorAdapter_1.idXML"/>
509 </conditional> 526 </conditional>
510 <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 527 <output name="out" value="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"/> 528 <output name="out_pin" value="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
512 <param name="out_type" value="idXML"/> 529 <param name="out_type" value="idXML"/>
513 <param name="enzyme" value="trypsin"/> 530 <param name="enzyme" value="trypsin"/>
514 <param name="peptide_level_fdrs" value="false"/> 531 <param name="peptide_level_fdrs" value="false"/>
515 <param name="protein_level_fdrs" value="false"/> 532 <param name="protein_level_fdrs" value="false"/>
516 <param name="osw_level" value="ms2"/> 533 <param name="osw_level" value="ms2"/>
519 <output name="ctd_out" ftype="xml"> 536 <output name="ctd_out" ftype="xml">
520 <assert_contents> 537 <assert_contents>
521 <is_valid_xml/> 538 <is_valid_xml/>
522 </assert_contents> 539 </assert_contents>
523 </output> 540 </output>
541 <assert_stdout>
542 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
543 </assert_stdout>
524 </test> 544 </test>
525 </tests> 545 </tests>
526 <help><![CDATA[Facilitate input to Percolator and reintegrate. 546 <help><![CDATA[Facilitate input to Percolator and reintegrate.
527 547
528 548
529 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PercolatorAdapter.html]]></help> 549 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PercolatorAdapter.html]]></help>
530 <expand macro="references"/> 550 <expand macro="references"/>
531 </tool> 551 </tool>