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comparison PercolatorAdapter.xml @ 0:f4739b6254a0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 06:23:24 -0400
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children 511f2f26bab8
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-1:000000000000 0:f4739b6254a0
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.-->
3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="PercolatorAdapter" name="PercolatorAdapter" version="2.3.0">
5 <description>Facilitate input to Percolator and reintegrate.</description>
6 <macros>
7 <token name="@EXECUTABLE@">PercolatorAdapter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command detect_errors="aggressive"><![CDATA[PercolatorAdapter
14
15 -in
16 #for token in $param_in:
17 $token
18 #end for
19 -in_decoy
20 #for token in $param_in_decoy:
21 $token
22 #end for
23 #if $param_out:
24 -out $param_out
25 #end if
26 #if $param_mzid_out:
27 -mzid_out $param_mzid_out
28 #end if
29 #if $param_enzyme:
30 -enzyme
31 #if " " in str($param_enzyme):
32 "$param_enzyme"
33 #else
34 $param_enzyme
35 #end if
36 #end if
37 #if $param_percolator_executable:
38 -percolator_executable $param_percolator_executable
39 #end if
40 #if $param_peptide_level_fdrs:
41 -peptide-level-fdrs
42 #end if
43 #if $param_protein_level_fdrs:
44 -protein-level-fdrs
45 #end if
46 #if $param_weights:
47 -weights $param_weights
48 #end if
49 #if $adv_opts.adv_opts_selector=='advanced':
50 #if $adv_opts.param_generic_feature_set:
51 -generic-feature-set
52 #end if
53 #if $adv_opts.param_subset_max_train:
54 -subset-max-train $adv_opts.param_subset_max_train
55 #end if
56 #if $adv_opts.param_cpos:
57 -cpos $adv_opts.param_cpos
58 #end if
59 #if $adv_opts.param_cneg:
60 -cneg $adv_opts.param_cneg
61 #end if
62 #if $adv_opts.param_testFDR:
63 -testFDR $adv_opts.param_testFDR
64 #end if
65 #if $adv_opts.param_trainFDR:
66 -trainFDR $adv_opts.param_trainFDR
67 #end if
68 #if $adv_opts.param_maxiter:
69 -maxiter $adv_opts.param_maxiter
70 #end if
71 #if $adv_opts.param_quick_validation:
72 -quick-validation
73 #end if
74 #if $adv_opts.param_init_weights:
75 -init-weights $adv_opts.param_init_weights
76 #end if
77 #if $adv_opts.param_default_direction:
78 -default-direction "$adv_opts.param_default_direction"
79 #end if
80 #if $adv_opts.param_verbose:
81 -verbose $adv_opts.param_verbose
82 #end if
83 #if $adv_opts.param_unitnorm:
84 -unitnorm
85 #end if
86 #if $adv_opts.param_test_each_iteration:
87 -test-each-iteration
88 #end if
89 #if $adv_opts.param_override:
90 -override
91 #end if
92 #if $adv_opts.param_seed:
93 -seed $adv_opts.param_seed
94 #end if
95 #if $adv_opts.param_doc:
96 -doc $adv_opts.param_doc
97 #end if
98 #if $adv_opts.param_klammer:
99 -klammer
100 #end if
101 #if $adv_opts.param_fasta:
102 -fasta $adv_opts.param_fasta
103 #end if
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>
116 <param name="param_in" type="data" format="mzid,idxml" multiple="true" optional="False" size="30" label="Input file(s)" help="(-in) ">
117 <sanitizer>
118 <valid initial="string.printable">
119 <remove value="'"/>
120 <remove value="&quot;"/>
121 </valid>
122 </sanitizer>
123 </param>
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) ">
125 <sanitizer>
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>
134 <option value="elastase">elastase</option>
135 <option value="pepsin">pepsin</option>
136 <option value="proteinasek">proteinasek</option>
137 <option value="thermolysin">thermolysin</option>
138 <option value="chymotrypsin">chymotrypsin</option>
139 <option value="lys-n">lys-n</option>
140 <option value="lys-c">lys-c</option>
141 <option value="arg-c">arg-c</option>
142 <option value="asp-n">asp-n</option>
143 <option value="glu-c">glu-c</option>
144 <option value="trypsin" selected="true">trypsin</option>
145 </param>
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'"/>
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) "/>
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"/>
149 <expand macro="advanced_options">
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"/>
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"/>
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"/>
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"/>
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) "/>
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"/>
156 <param name="param_maxiter" type="integer" value="10" label="Maximal number of iterations" help="(-maxiter) "/>
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) "/>
158 <param name="param_init_weights" type="data" format="txt" label="Read initial weights to the given file" help="(-init-weights) "/>
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) ">
160 <sanitizer>
161 <valid initial="string.printable">
162 <remove value="'"/>
163 <remove value="&quot;"/>
164 </valid>
165 </sanitizer>
166 </param>
167 <param name="param_verbose" type="integer" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help="(-verbose) "/>
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) "/>
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) "/>
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) "/>
171 <param name="param_seed" type="integer" value="1" label="Setting seed of the random number generato" help="(-seed) "/>
172 <param name="param_doc" type="integer" value="0" label="Include description of correct features" help="(-doc) "/>
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"/>
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) "/>
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) ">
176 <sanitizer>
177 <valid initial="string.printable">
178 <remove value="'"/>
179 <remove value="&quot;"/>
180 </valid>
181 </sanitizer>
182 </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) "/>
184 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
185 </expand>
186 </inputs>
187 <outputs>
188 <data name="param_out" format="idxml"/>
189 <data name="param_mzid_out" format="mzid"/>
190 <data name="param_weights" format="data"/>
191 </outputs>
192 <help>Facilitate input to Percolator and reintegrate.
193
194
195 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PercolatorAdapter.html</help>
196 </tool>