comparison RTEvaluation.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

3:ec62782f6c68

<?xml version='1.0' encoding='UTF-8'?>
<tool id="RTEvaluation" name="RTEvaluation" version="1.12.0">
  <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
  <macros>
    <token name="@EXECUTABLE@">RTEvaluation</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>RTEvaluation

-in ${param_in}
-out ${param_out}
-sequences_file ${param_sequences_file}
${param_latex}
-p_value_dim_1 ${param_p_value_dim_1}
-p_value_dim_2 ${param_p_value_dim_2}
-threads \${GALAXY_SLOTS:-24} 
</command>
  <inputs>
    <param name="param_in" type="data" format="idXML" optional="False" label="input file" help="(-in)"/>
    <param name="param_sequences_file" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences.#br#All peptides that are not a substring of a sequence in this file are considered as false" help="(-sequences_file)"/>
    <param name="param_latex" type="boolean" truevalue="-latex true" falsevalue="-latex false" checked="false" optional="True" label="indicates whether the output file format of the table should be latex or csv" help="(-latex)"/>
    <param name="param_p_value_dim_1" type="float" min="0.0" max="1.0" optional="True" value="0.01" label="Significance level of first dimension RT filter" help="(-p_value_dim_1)"/>
    <param name="param_p_value_dim_2" type="float" min="0.0" max="1.0" optional="True" value="0.05" label="Significance level of second dimension RT filter" help="(-p_value_dim_2)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output file " format="tabular"/>
  </outputs>
  <help>**What it does**

Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html

@REFERENCES@
</help>
</tool>

4:6ead64a594bd

<?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="RTEvaluation" name="RTEvaluation" version="2.0.0">
    <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
    <macros>
      <token name="@EXECUTABLE@">RTEvaluation</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>RTEvaluation

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_sequences_file:
  -sequences_file $param_sequences_file
#end if
#if $param_latex:
  -latex
#end if
#if $param_p_value_dim_1:
  -p_value_dim_1 $param_p_value_dim_1
#end if
#if $param_p_value_dim_2:
  -p_value_dim_2 $param_p_value_dim_2
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
      <param format="fasta" help="(-sequences_file) &lt;br&gt;All peptides that are not a substring of a sequence in this file are considered as false" label="Filename of a FASTA file containing protein sequences" name="param_sequences_file" optional="True" type="data"/>
      <param checked="false" falsevalue="" help="(-latex) " label="indicates whether the output file format of the table should be latex or csv" name="param_latex" optional="True" truevalue="-latex" type="boolean"/>
      <param help="(-p_value_dim_1) " label="Significance level of first dimension RT filte" max="1.0" min="0.0" name="param_p_value_dim_1" optional="True" type="float" value="0.01"/>
      <param help="(-p_value_dim_2) " label="Significance level of second dimension RT filte" max="1.0" min="0.0" name="param_p_value_dim_2" optional="True" type="float" value="0.05"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="tabular" name="param_out"/>
    </outputs>
    <help>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.


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