comparison TopPerc.xml @ 1:a6574e6fc144 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

0:fc7bbbcd8194

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="TopPerc" name="TopPerc" version="2.1.0">
  <description>Facilitate input to Percolator and reintegrate.</description>
  <macros>
    <token name="@EXECUTABLE@">TopPerc</token>
    <import>macros.xml</import>
  </macros>

  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_percolator_executable" type="data" format="text" label="Path to the percolator binary" help="(-percolator_executable) "/>
    <param name="param_in_target" type="data" format="mzid" optional="False" label="Input target file" help="(-in_target) "/>
    <param name="param_in_decoy" type="data" format="mzid" optional="False" label="Input decoy file" help="(-in_decoy) "/>
    <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) ">
      <sanitizer>
        <valid initial="string.printable">

    <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"/>
    <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"/>
    <param name="param_i" type="integer" value="0" label="Maximal number of iterations" help="(-i) "/>
    <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) "/>
    <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"/>
    <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"/>
    <param name="param_W" type="data" format="text" label="Read initial weights to the given file" help="(-W) "/>
    <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) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>

    <data name="param_B" format="data"/>
  </outputs>
  <help>Facilitate input to Percolator and reintegrate.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_TopPerc.html</help>
</tool>

1:a6574e6fc144

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="TopPerc" name="TopPerc" version="2.2.0.1">
  <description>Facilitate input to Percolator and reintegrate.</description>
  <macros>
    <token name="@EXECUTABLE@">TopPerc</token>
    <import>macros.xml</import>
  </macros>

  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_percolator_executable" type="data" format="txt" label="Path to the percolator binary" help="(-percolator_executable) "/>
    <param name="param_in_target" type="data" format="mzid" optional="False" label="Input target file" help="(-in_target) "/>
    <param name="param_in_decoy" type="data" format="mzid" optional="False" label="Input decoy file" help="(-in_decoy) "/>
    <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) ">
      <sanitizer>
        <valid initial="string.printable">

    <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"/>
    <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"/>
    <param name="param_i" type="integer" value="0" label="Maximal number of iterations" help="(-i) "/>
    <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) "/>
    <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"/>
    <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"/>
    <param name="param_W" type="data" format="txt" label="Read initial weights to the given file" help="(-W) "/>
    <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) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>

    <data name="param_B" format="data"/>
  </outputs>
  <help>Facilitate input to Percolator and reintegrate.


For more information, visit http://ftp.mi.fu-berlin.de/pub/OpenMS/develop-documentation/html/TOPP_TopPerc.html</help>
</tool>