comparison MapStatistics.xml @ 13:a3ae12b9217a draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"

12:a46a12fedf7f

<?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 CTDConverter.-->
<!--Proposed Tool Section: [File Handling]-->
<tool id="MapStatistics" name="MapStatistics" version="2.3.0">
  <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 detect_errors="aggressive"><![CDATA[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
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="featurexml,consensusxml" optional="False" label="Input file" help="(-in) "/>
    <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" display="radio" type="boolean" truevalue="-m" falsevalue="" checked="false" optional="True" label="Show meta information about the whole experiment" help="(-m) "/>
    <param name="param_p" display="radio" type="boolean" truevalue="-p" falsevalue="" checked="false" optional="True" label="Shows data processing information" help="(-p) "/>
    <param name="param_s" display="radio" type="boolean" truevalue="-s" falsevalue="" checked="false" optional="True" label="Computes a summary statistics of intensities, qualities, and widths" help="(-s) "/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="txt"/>
  </outputs>
  <help>Extract extended statistics on the features of a map for quality control.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MapStatistics.html</help>
</tool>

13:a3ae12b9217a

<?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 CTDConverter.-->
<!--Proposed Tool Section: [File Handling]-->
<tool id="MapStatistics" name="MapStatistics" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Extract extended statistics on the features of a map for quality control.</description>
  <macros>
    <token name="@EXECUTABLE@">MapStatistics</token>
    <import>macros.xml</import>
    <import>macros_autotest.xml</import>
    <import>macros_test.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir out &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-out
'out/output.${gxy2omsext("txt")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("txt")}' '$out'
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="Input file" help=" select consensusxml,featurexml data sets(s)"/>
    <param name="n" argument="-n" type="integer" optional="true" min="1" max="100" value="4" label="Report separate statistics for each of n RT slices of the map" help=""/>
    <param name="m" argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
    <param name="p" argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
    <param name="s" argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a summary statistics of intensities, qualities, and widths" help=""/>
    <expand macro="adv_opts_macro">
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <expand macro="autotest_MapStatistics"/>
    <expand macro="manutest_MapStatistics"/>
  </tests>
  <help><![CDATA[Extract extended statistics on the features of a map for quality control.


For more information, visit http://www.openms.de/documentation/TOPP_MapStatistics.html]]></help>
  <expand macro="references"/>
</tool>