annotate ClusterMassTracesByPrecursor.xml @ 5:f0c018228cec draft default tip

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

<!--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="ClusterMassTracesByPrecursor" name="ClusterMassTracesByPrecursor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile</description>
  <macros>
    <token name="@EXECUTABLE@">ClusterMassTracesByPrecursor</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in_ms1 &&
cp '$in_ms1' 'in_ms1/${re.sub("[^\w\-_]", "_", $in_ms1.element_identifier)}.$gxy2omsext($in_ms1.ext)' &&
mkdir in_swath &&
cp '$in_swath' 'in_swath/${re.sub("[^\w\-_]", "_", $in_swath.element_identifier)}.$gxy2omsext($in_swath.ext)' &&
mkdir out &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in_ms1
'in_ms1/${re.sub("[^\w\-_]", "_", $in_ms1.element_identifier)}.$gxy2omsext($in_ms1.ext)'
-in_swath
'in_swath/${re.sub("[^\w\-_]", "_", $in_swath.element_identifier)}.$gxy2omsext($in_swath.ext)'
-out
'out/output.${gxy2omsext("mzml")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("mzml")}' '$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 argument="-in_ms1" type="data" format="consensusxml" label="MS1 mass traces" help=" select consensusxml data sets(s)"/>
    <param argument="-in_swath" type="data" format="consensusxml" label="MS2 / SWATH mass traces" help=" select consensusxml data sets(s)"/>
    <param argument="-assign_unassigned_to_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign unassigned MS2 fragments to all precursors (only for ms1_centrif)" help=""/>
    <param argument="-min_pearson_correlation" type="float" value="0.7" label="Minimal pearson correlation score to match elution profiles to each othe" help=""/>
    <param argument="-max_lag" type="integer" value="1" label="Maximal lag" help="(e.g. by how many spectra the peak may be shifted at most). This parameter will depend on your chromatographic setup but a number between 1 and 3 is usually sensible"/>
    <param argument="-min_nr_ions" type="integer" value="3" label="Minimal number of ions to report a spectrum" help=""/>
    <param argument="-max_rt_apex_difference" type="float" value="5.0" label="Maximal difference of the apex in retention time (in seconds)" help="This is a hard parameter, all profiles further away will not be considered at all"/>
    <param argument="-swath_lower" type="float" value="0.0" label="Swath lower isolation window" help=""/>
    <param argument="-swath_upper" type="float" value="0.0" label="Swath upper isolation window" help=""/>
    <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>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
    <data name="ctd_out" format="xml" label="${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">
      <!-- test with arbitarily chosen consensusXML -->
      <param name="adv_opts|test" value="true"/>
      <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
      <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
      <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/>
    </test>
  </tests>
  <help><![CDATA[Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.


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