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comparison PercolatorAdapter.xml @ 1:511f2f26bab8 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 22:20:07 +0000
parents f4739b6254a0
children 94b78ce391d5
comparison
equal deleted inserted replaced
0:f4739b6254a0 1:511f2f26bab8
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="2.3.0"> 4 <tool id="PercolatorAdapter" name="PercolatorAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[PercolatorAdapter 15 @EXT_FOO@
14 16 #import re
15 -in 17
16 #for token in $param_in: 18 ## Preprocessing
17 $token 19 #if $in:
18 #end for 20 mkdir in &&
19 -in_decoy 21 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
20 #for token in $param_in_decoy: 22 #end if
21 $token 23 #if $in_decoy:
22 #end for 24 mkdir in_decoy &&
23 #if $param_out: 25 ${ ' '.join(["ln -s '%s' 'in_decoy/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_decoy if _]) }
24 -out $param_out 26 #end if
25 #end if 27 #if $in_osw:
26 #if $param_mzid_out: 28 mkdir in_osw &&
27 -mzid_out $param_mzid_out 29 ln -s '$in_osw' 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)' &&
28 #end if 30 #end if
29 #if $param_enzyme: 31 mkdir out &&
30 -enzyme 32 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
31 #if " " in str($param_enzyme): 33 mkdir out_pin &&
32 "$param_enzyme" 34 #end if
33 #else 35 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
34 $param_enzyme 36 mkdir weights &&
35 #end if 37 #end if
36 #end if 38 #if $adv_opts_cond.adv_opts_selector=='advanced':
37 #if $param_percolator_executable: 39 #if $adv_opts_cond.init_weights:
38 -percolator_executable $param_percolator_executable 40 mkdir adv_opts_cond.init_weights &&
39 #end if 41 ln -s '$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)' &&
40 #if $param_peptide_level_fdrs: 42 #end if
41 -peptide-level-fdrs 43 #if $adv_opts_cond.fasta:
42 #end if 44 mkdir adv_opts_cond.fasta &&
43 #if $param_protein_level_fdrs: 45 ln -s '$adv_opts_cond.fasta' 'adv_opts_cond.fasta/${re.sub("[^\w\-_]", "_", $adv_opts_cond.fasta.element_identifier)}.$gxy2omsext($adv_opts_cond.fasta.ext)' &&
44 -protein-level-fdrs 46 #end if
45 #end if 47 #end if
46 #if $param_weights: 48
47 -weights $param_weights 49 ## Main program call
48 #end if 50
49 #if $adv_opts.adv_opts_selector=='advanced': 51 set -o pipefail &&
50 #if $adv_opts.param_generic_feature_set: 52 @EXECUTABLE@ -write_ctd ./ &&
51 -generic-feature-set 53 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
52 #end if 54 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
53 #if $adv_opts.param_subset_max_train: 55 #if $in:
54 -subset-max-train $adv_opts.param_subset_max_train 56 -in
55 #end if 57 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
56 #if $adv_opts.param_cpos: 58 #end if
57 -cpos $adv_opts.param_cpos 59 #if $in_decoy:
58 #end if 60 -in_decoy
59 #if $adv_opts.param_cneg: 61 ${' '.join(["'in_decoy/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_decoy if _])}
60 -cneg $adv_opts.param_cneg 62 #end if
61 #end if 63 #if $in_osw:
62 #if $adv_opts.param_testFDR: 64 -in_osw
63 -testFDR $adv_opts.param_testFDR 65 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)'
64 #end if 66 #end if
65 #if $adv_opts.param_trainFDR: 67 -out
66 -trainFDR $adv_opts.param_trainFDR 68 'out/output.${out_type}'
67 #end if 69 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
68 #if $adv_opts.param_maxiter: 70 -out_pin
69 -maxiter $adv_opts.param_maxiter 71 'out_pin/output.${gxy2omsext("tabular")}'
70 #end if 72 #end if
71 #if $adv_opts.param_quick_validation: 73 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
72 -quick-validation 74 -weights
73 #end if 75 'weights/output.${gxy2omsext("txt")}'
74 #if $adv_opts.param_init_weights: 76 #end if
75 -init-weights $adv_opts.param_init_weights 77 #if $adv_opts_cond.adv_opts_selector=='advanced':
76 #end if 78 #if $adv_opts_cond.init_weights:
77 #if $adv_opts.param_default_direction: 79 -init-weights
78 -default-direction "$adv_opts.param_default_direction" 80 'adv_opts_cond.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts_cond.init_weights.element_identifier)}.$gxy2omsext($adv_opts_cond.init_weights.ext)'
79 #end if 81 #end if
80 #if $adv_opts.param_verbose: 82 #if $adv_opts_cond.fasta:
81 -verbose $adv_opts.param_verbose 83 -fasta
82 #end if 84 'adv_opts_cond.fasta/${re.sub("[^\w\-_]", "_", $adv_opts_cond.fasta.element_identifier)}.$gxy2omsext($adv_opts_cond.fasta.ext)'
83 #if $adv_opts.param_unitnorm: 85 #end if
84 -unitnorm 86 #end if
85 #end if 87 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
86 #if $adv_opts.param_test_each_iteration: 88 | tee '$stdout'
87 -test-each-iteration 89 #end if
88 #end if 90
89 #if $adv_opts.param_override: 91 ## Postprocessing
90 -override 92 && mv 'out/output.${out_type}' '$out'
91 #end if 93 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
92 #if $adv_opts.param_seed: 94 && mv 'out_pin/output.${gxy2omsext("tabular")}' '$out_pin'
93 -seed $adv_opts.param_seed 95 #end if
94 #end if 96 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
95 #if $adv_opts.param_doc: 97 && mv 'weights/output.${gxy2omsext("txt")}' '$weights'
96 -doc $adv_opts.param_doc 98 #end if
97 #end if 99 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
98 #if $adv_opts.param_klammer: 100 && mv '@EXECUTABLE@.ctd' '$ctd_out'
99 -klammer 101 #end if]]></command>
100 #end if 102 <configfiles>
101 #if $adv_opts.param_fasta: 103 <inputs name="args_json" data_style="paths"/>
102 -fasta $adv_opts.param_fasta 104 <configfile name="hardcoded_json"><![CDATA[{"percolator_executable": "percolator", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
103 #end if 105 </configfiles>
104 #if $adv_opts.param_decoy_pattern:
105 -decoy-pattern "$adv_opts.param_decoy_pattern"
106 #end if
107 #if $adv_opts.param_post_processing_tdc:
108 -post-processing-tdc
109 #end if
110 #if $adv_opts.param_force:
111 -force
112 #end if
113 #end if
114 ]]></command>
115 <inputs> 106 <inputs>
116 <param name="param_in" type="data" format="mzid,idxml" multiple="true" optional="False" size="30" label="Input file(s)" help="(-in) "> 107 <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)"/>
117 <sanitizer> 108 <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)"/>
118 <valid initial="string.printable"> 109 <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)"/>
119 <remove value="'"/> 110 <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="">
120 <remove value="&quot;"/> 111 <option value="idXML">idxml</option>
121 </valid> 112 <option value="mzid">mzid</option>
122 </sanitizer> 113 <option value="osw">osw</option>
123 </param> 114 <expand macro="list_string_san"/>
124 <param name="param_in_decoy" type="data" format="mzid,idxml" multiple="true" optional="True" size="30" label="Input decoy file(s) in case of separate searches" help="(-in_decoy) "> 115 </param>
125 <sanitizer> 116 <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="">
126 <valid initial="string.printable">
127 <remove value="'"/>
128 <remove value="&quot;"/>
129 </valid>
130 </sanitizer>
131 </param>
132 <param name="param_enzyme" type="select" optional="False" value="trypsin" label="Type of enzyme: no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin" help="(-enzyme) ">
133 <option value="no_enzyme">no_enzyme</option> 117 <option value="no_enzyme">no_enzyme</option>
134 <option value="elastase">elastase</option> 118 <option value="elastase">elastase</option>
135 <option value="pepsin">pepsin</option> 119 <option value="pepsin">pepsin</option>
136 <option value="proteinasek">proteinasek</option> 120 <option value="proteinasek">proteinasek</option>
137 <option value="thermolysin">thermolysin</option> 121 <option value="thermolysin">thermolysin</option>
140 <option value="lys-c">lys-c</option> 124 <option value="lys-c">lys-c</option>
141 <option value="arg-c">arg-c</option> 125 <option value="arg-c">arg-c</option>
142 <option value="asp-n">asp-n</option> 126 <option value="asp-n">asp-n</option>
143 <option value="glu-c">glu-c</option> 127 <option value="glu-c">glu-c</option>
144 <option value="trypsin" selected="true">trypsin</option> 128 <option value="trypsin" selected="true">trypsin</option>
145 </param> 129 <option value="trypsinp">trypsinp</option>
146 <param name="param_percolator_executable" type="data" format="txt" value="percolator" label="Percolator executable of the installation" help="(-percolator_executable) e.g. 'percolator.exe'"/> 130 <expand macro="list_string_san"/>
147 <param name="param_peptide_level_fdrs" display="radio" type="boolean" truevalue="-peptide-level-fdrs" falsevalue="" checked="false" optional="True" label="Calculate peptide-level FDRs instead of PSM-level FDRs" help="(-peptide-level-fdrs) "/> 131 </param>
148 <param name="param_protein_level_fdrs" display="radio" type="boolean" truevalue="-protein-level-fdrs" falsevalue="" checked="false" optional="True" label="Use the picked protein-level FDR to infer protein probabilities" help="(-protein-level-fdrs) Use the -fasta option and -decoy-pattern to set the Fasta file and decoy pattern"/> 132 <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=""/>
149 <expand macro="advanced_options"> 133 <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"/>
150 <param name="param_generic_feature_set" display="radio" type="boolean" truevalue="-generic-feature-set" falsevalue="" checked="false" optional="True" label="Use only generic (i.e" help="(-generic-feature-set) not search engine specific) features. Generating search engine specific features for common search engines by PSMFeatureExtractor will typically boost the identification rate significantly"/> 134 <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="">
151 <param name="param_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="(-subset-max-train) Recommended when analyzing huge numbers (&gt;1 million) of PSMs. When set to 0, all PSMs are used for training as normal"/> 135 <expand macro="list_string_san"/>
152 <param name="param_cpos" type="float" value="0.0" label="Cpos, penalty for mistakes made on positive examples" help="(-cpos) Set by cross validation if not specified"/> 136 </param>
153 <param name="param_cneg" type="float" value="0.0" label="Cneg, penalty for mistakes made on negative examples" help="(-cneg) Set by cross validation if not specified"/> 137 <param name="score_type" argument="-score_type" display="radio" type="select" optional="false" label="Type of the peptide main score" help="">
154 <param name="param_testFDR" type="float" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help="(-testFDR) "/> 138 <option value="q-value" selected="true">q-value</option>
155 <param name="param_trainFDR" type="float" value="0.01" label="False discovery rate threshold to define positive examples in training" help="(-trainFDR) Set to testFDR if 0"/> 139 <option value="pep">pep</option>
156 <param name="param_maxiter" type="integer" value="10" label="Maximal number of iterations" help="(-maxiter) "/> 140 <option value="svm">svm</option>
157 <param name="param_quick_validation" display="radio" type="boolean" truevalue="-quick-validation" falsevalue="" checked="false" optional="True" label="Quicker execution by reduced internal cross-validation" help="(-quick-validation) "/> 141 <expand macro="list_string_san"/>
158 <param name="param_init_weights" type="data" format="txt" label="Read initial weights to the given file" help="(-init-weights) "/> 142 </param>
159 <param name="param_default_direction" type="text" size="30" label="The most informative feature given as the feature name, can be negated to indicate that a lower value is bette" help="(-default-direction) "> 143 <expand macro="adv_opts_macro">
160 <sanitizer> 144 <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"/>
161 <valid initial="string.printable"> 145 <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"/>
162 <remove value="'"/> 146 <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"/>
163 <remove value="&quot;"/> 147 <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"/>
164 </valid> 148 <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=""/>
165 </sanitizer> 149 <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"/>
150 <param name="maxiter" argument="-maxiter" type="integer" optional="true" value="10" label="Maximal number of iterations" help=""/>
151 <param name="quick_validation" argument="-quick-validation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Quicker execution by reduced internal cross-validation" help=""/>
152 <param name="init_weights" argument="-init-weights" type="data" format="txt" optional="true" label="Read initial weights to the given file" help=" select txt data sets(s)"/>
153 <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="">
154 <expand macro="list_string_san"/>
166 </param> 155 </param>
167 <param name="param_verbose" type="integer" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help="(-verbose) "/> 156 <param name="verbose" argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/>
168 <param name="param_unitnorm" display="radio" type="boolean" truevalue="-unitnorm" falsevalue="" checked="false" optional="True" label="Use unit normalization [0-1] instead of standard deviation normalization" help="(-unitnorm) "/> 157 <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=""/>
169 <param name="param_test_each_iteration" display="radio" type="boolean" truevalue="-test-each-iteration" falsevalue="" checked="false" optional="True" label="Measure performance on test set each iteration" help="(-test-each-iteration) "/> 158 <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=""/>
170 <param name="param_override" display="radio" type="boolean" truevalue="-override" falsevalue="" checked="false" optional="True" label="Override error check and do not fall back on default score vector in case of suspect score vecto" help="(-override) "/> 159 <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=""/>
171 <param name="param_seed" type="integer" value="1" label="Setting seed of the random number generato" help="(-seed) "/> 160 <param name="seed" argument="-seed" type="integer" optional="true" value="1" label="Setting seed of the random number generato" help=""/>
172 <param name="param_doc" type="integer" value="0" label="Include description of correct features" help="(-doc) "/> 161 <param name="doc" argument="-doc" type="integer" optional="true" value="0" label="Include description of correct features" help=""/>
173 <param name="param_klammer" display="radio" type="boolean" truevalue="-klammer" falsevalue="" checked="false" optional="True" label="Retention time features calculated as in Klammer et al" help="(-klammer) Only available if -doc is set"/> 162 <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"/>
174 <param name="param_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="(-fasta) "/> 163 <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)"/>
175 <param name="param_decoy_pattern" type="text" size="30" 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="(-decoy-pattern) "> 164 <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="">
176 <sanitizer> 165 <expand macro="list_string_san"/>
177 <valid initial="string.printable">
178 <remove value="'"/>
179 <remove value="&quot;"/>
180 </valid>
181 </sanitizer>
182 </param> 166 </param>
183 <param name="param_post_processing_tdc" display="radio" type="boolean" truevalue="-post-processing-tdc" falsevalue="" checked="false" optional="True" label="Use target-decoy competition to assign q-values and PEPs" help="(-post-processing-tdc) "/> 167 <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=""/>
184 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 168 <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"/>
169 <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=""/>
170 <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=""/>
171 <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"/>
172 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
173 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
174 <expand macro="list_string_san"/>
175 </param>
185 </expand> 176 </expand>
177 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
178 <option value="out_pin_FLAG">out_pin (Enables the test mode (needed for internal use only))</option>
179 <option value="weights_FLAG">weights (Enables the test mode (needed for internal use only))</option>
180 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
181 </param>
186 </inputs> 182 </inputs>
187 <outputs> 183 <outputs>
188 <data name="param_out" format="idxml"/> 184 <data name="out" label="${tool.name} on ${on_string}: out">
189 <data name="param_mzid_out" format="mzid"/> 185 <change_format>
190 <data name="param_weights" format="data"/> 186 <when input="out_type" value="idXML" format="idxml"/>
187 <when input="out_type" value="mzid" format="mzid"/>
188 <when input="out_type" value="osw" format="osw"/>
189 </change_format>
190 </data>
191 <data name="out_pin" label="${tool.name} on ${on_string}: out_pin" format="tabular">
192 <filter>OPTIONAL_OUTPUTS is not None and "out_pin_FLAG" in OPTIONAL_OUTPUTS</filter>
193 </data>
194 <data name="weights" label="${tool.name} on ${on_string}: weights" format="txt">
195 <filter>OPTIONAL_OUTPUTS is not None and "weights_FLAG" in OPTIONAL_OUTPUTS</filter>
196 </data>
197 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
198 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
199 </data>
191 </outputs> 200 </outputs>
192 <help>Facilitate input to Percolator and reintegrate. 201 <tests>
193 202 <expand macro="autotest_PercolatorAdapter"/>
194 203 <expand macro="manutest_PercolatorAdapter"/>
195 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PercolatorAdapter.html</help> 204 </tests>
205 <help><![CDATA[Facilitate input to Percolator and reintegrate.
206
207
208 For more information, visit http://www.openms.de/documentation/TOPP_PercolatorAdapter.html]]></help>
209 <expand macro="references"/>
196 </tool> 210 </tool>