comparison MapStatistics.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="MapStatistics" name="MapStatistics" version="1.12.0">
  <description>Extract extended statistics on the features of a map for quality control.</description>
  <macros>
    <token name="@EXECUTABLE@">MapStatistics</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MapStatistics

-in ${param_in}
-in_type ${param_in_type}
-out ${param_out}
-n ${param_n}
${param_m}
${param_p}
${param_s}
-threads \${GALAXY_SLOTS:-24} 
</command>
  <inputs>
    <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" label="Input file" help="(-in)"/>
    <param name="param_in_type" type="select" optional="True" label="Input file type -- default: determined from file extension or content" help="(-in_type)">
      <option value="featureXML">featureXML</option>
      <option value="consensusXML">consensusXML</option>
    </param>
    <param name="param_n" type="integer" min="1" max="100" optional="True" value="4" label="Report separate statistics for each of n RT slices of the map." help="(-n)"/>
    <param name="param_m" type="boolean" truevalue="-m true" falsevalue="-m false" checked="false" optional="True" label="Show meta information about the whole experiment" help="(-m)"/>
    <param name="param_p" type="boolean" truevalue="-p true" falsevalue="-p false" checked="false" optional="True" label="Shows data processing information" help="(-p)"/>
    <param name="param_s" type="boolean" truevalue="-s true" falsevalue="-s false" checked="false" optional="True" label="Computes a summary statistics of intensities, qualities, and widths" help="(-s)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Optional output txt file. If '-' or left out, the output is written to the command line." format="txt"/>
  </outputs>
  <help>**What it does**

Extract extended statistics on the features of a map for quality control.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapStatistics.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: [File Handling]-->
  <tool id="MapStatistics" name="MapStatistics" version="2.0.0">
    <description>Extract extended statistics on the features of a map for quality control.</description>
    <macros>
      <token name="@EXECUTABLE@">MapStatistics</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>MapStatistics

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_n:
  -n $param_n
#end if
#if $param_m:
  -m
#end if
#if $param_p:
  -p
#end if
#if $param_s:
  -s
#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,consensusxml" help="(-in) " label="Input file" name="param_in" optional="False" type="data"/>
      <param help="(-n) " label="Report separate statistics for each of n RT slices of the map" max="100" min="1" name="param_n" optional="True" type="integer" value="4"/>
      <param checked="false" falsevalue="" help="(-m) " label="Show meta information about the whole experiment" name="param_m" optional="True" truevalue="-m" type="boolean"/>
      <param checked="false" falsevalue="" help="(-p) " label="Shows data processing information" name="param_p" optional="True" truevalue="-p" type="boolean"/>
      <param checked="false" falsevalue="" help="(-s) " label="Computes a summary statistics of intensities, qualities, and widths" name="param_s" optional="True" truevalue="-s" type="boolean"/>
      <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="txt" name="param_out"/>
    </outputs>
    <help>Extract extended statistics on the features of a map for quality control.


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