comparison OpenSwathRewriteToFeatureXML.xml @ 14:77f01ffce2b7 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

13:b956337a7473

<?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: [Targeted Experiments]-->
<tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>

#import re

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

## Main program call

set -o pipefail &&

    <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 argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help=" select csv data sets(s)"/>
    <param argument="-featureXML" type="data" format="featurexml" optional="false" label="input featureXML file" help=" select featurexml data sets(s)"/>
    <param argument="-FDR_cutoff" type="float" optional="true" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
    <expand macro="adv_opts_macro">
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>

    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
    <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
    <param name="adv_opts|test" value="true"/>
    <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/>
  </test>
</tests>
  <help><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML.


For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathRewriteToFeatureXML.html]]></help>
  <expand macro="references"/>
</tool>

14:77f01ffce2b7

<!--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: [Targeted Experiments and OpenSWATH]-->
<tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Combines featureXML and mProphet tsv to FDR filtered featureXML</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>

#import re

## Preprocessing
#if $csv:
  mkdir csv &&
  cp '$csv' 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)' &&
#end if
mkdir featureXML &&
cp '$featureXML' 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)' &&
mkdir out &&

## Main program call

set -o pipefail &&

    <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 argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help=" select csv data sets(s)"/>
    <param argument="-featureXML" type="data" format="featurexml" label="input featureXML file" help=" select featurexml data sets(s)"/>
    <param argument="-FDR_cutoff" type="float" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
    <expand macro="adv_opts_macro">
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>

    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <test expect_num_outputs="1">
      <!-- same input as used in the MSGF+Adapter -->
      <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
      <param name="adv_opts|test" value="true"/>
      <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/>
    </test>
  </tests>
  <help><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML.


For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathRewriteToFeatureXML.html]]></help>
  <expand macro="references"/>
</tool>