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comparison TopPerc.xml @ 1:a6574e6fc144 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 10:03:14 -0400
parents fc7bbbcd8194
children
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0:fc7bbbcd8194 1:a6574e6fc144
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 CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="TopPerc" name="TopPerc" version="2.1.0"> 4 <tool id="TopPerc" name="TopPerc" version="2.2.0.1">
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@">TopPerc</token> 7 <token name="@EXECUTABLE@">TopPerc</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
158 -force 158 -force
159 #end if 159 #end if
160 #end if 160 #end if
161 </command> 161 </command>
162 <inputs> 162 <inputs>
163 <param name="param_percolator_executable" type="data" format="text" label="Path to the percolator binary" help="(-percolator_executable) "/> 163 <param name="param_percolator_executable" type="data" format="txt" label="Path to the percolator binary" help="(-percolator_executable) "/>
164 <param name="param_in_target" type="data" format="mzid" optional="False" label="Input target file" help="(-in_target) "/> 164 <param name="param_in_target" type="data" format="mzid" optional="False" label="Input target file" help="(-in_target) "/>
165 <param name="param_in_decoy" type="data" format="mzid" optional="False" label="Input decoy file" help="(-in_decoy) "/> 165 <param name="param_in_decoy" type="data" format="mzid" optional="False" label="Input decoy file" help="(-in_decoy) "/>
166 <param name="param_enzyme" type="text" size="30" 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) "> 166 <param name="param_enzyme" type="text" size="30" 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) ">
167 <sanitizer> 167 <sanitizer>
168 <valid initial="string.printable"> 168 <valid initial="string.printable">
178 <param name="param_F" type="float" value="0.01" label="False discovery rate threshold to define positive examples in training" help="(-F) Set by cross validation if 0. Default is 0.01"/> 178 <param name="param_F" type="float" value="0.01" label="False discovery rate threshold to define positive examples in training" help="(-F) Set by cross validation if 0. Default is 0.01"/>
179 <param name="param_t" type="float" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help="(-t) Default is 0.01"/> 179 <param name="param_t" type="float" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help="(-t) Default is 0.01"/>
180 <param name="param_i" type="integer" value="0" label="Maximal number of iterations" help="(-i) "/> 180 <param name="param_i" type="integer" value="0" label="Maximal number of iterations" help="(-i) "/>
181 <param name="param_x" display="radio" type="boolean" truevalue="-x" falsevalue="" checked="false" optional="True" label="Quicker execution by reduced internal cross-validation" help="(-x) "/> 181 <param name="param_x" display="radio" type="boolean" truevalue="-x" falsevalue="" checked="false" optional="True" label="Quicker execution by reduced internal cross-validation" help="(-x) "/>
182 <param name="param_f" type="float" value="0.6" label="Fraction of the negative data set to be used as train set when only providing one negative set, remaining examples will be used as test set" help="(-f) Set to 0.6 by default"/> 182 <param name="param_f" type="float" value="0.6" label="Fraction of the negative data set to be used as train set when only providing one negative set, remaining examples will be used as test set" help="(-f) Set to 0.6 by default"/>
183 <param name="param_k" type="data" format="text" label="Input file given in the deprecated pin-xml format generated by" help="(-k) e.g. sqt2pin with the -k option"/> 183 <param name="param_k" type="data" format="txt" label="Input file given in the deprecated pin-xml format generated by" help="(-k) e.g. sqt2pin with the -k option"/>
184 <param name="param_W" type="data" format="text" label="Read initial weights to the given file" help="(-W) "/> 184 <param name="param_W" type="data" format="txt" label="Read initial weights to the given file" help="(-W) "/>
185 <param name="param_V" 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="(-V) "> 185 <param name="param_V" 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="(-V) ">
186 <sanitizer> 186 <sanitizer>
187 <valid initial="string.printable"> 187 <valid initial="string.printable">
188 <remove value="'"/> 188 <remove value="'"/>
189 <remove value="&quot;"/> 189 <remove value="&quot;"/>
235 <data name="param_B" format="data"/> 235 <data name="param_B" format="data"/>
236 </outputs> 236 </outputs>
237 <help>Facilitate input to Percolator and reintegrate. 237 <help>Facilitate input to Percolator and reintegrate.
238 238
239 239
240 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_TopPerc.html</help> 240 For more information, visit http://ftp.mi.fu-berlin.de/pub/OpenMS/develop-documentation/html/TOPP_TopPerc.html</help>
241 </tool> 241 </tool>