annotate MetaProSIP.xml @ 14:5f72a8fa935d 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: [Quantitation]-->
<tool id="MetaProSIP" name="MetaProSIP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Performs proteinSIP on peptide features for elemental flux analysis</description>
  <macros>
    <token name="@EXECUTABLE@">MetaProSIP</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_mzML &&
cp '$in_mzML' 'in_mzML/${re.sub("[^\w\-_]", "_", $in_mzML.element_identifier)}.$gxy2omsext($in_mzML.ext)' &&
mkdir in_fasta &&
cp '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' &&
mkdir out_csv &&
mkdir out_peptide_centric_csv &&
mkdir in_featureXML &&
cp '$in_featureXML' 'in_featureXML/${re.sub("[^\w\-_]", "_", $in_featureXML.element_identifier)}.$gxy2omsext($in_featureXML.ext)' &&

## Main program call

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

## Postprocessing
&& mv 'out_csv/output.${gxy2omsext("csv")}' '$out_csv'
&& mv 'out_peptide_centric_csv/output.${gxy2omsext("csv")}' '$out_peptide_centric_csv'
#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[{"r_executable": "R", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in_mzML" type="data" format="mzml" label="Centroided MS1 data" help=" select mzml data sets(s)"/>
    <param argument="-in_fasta" type="data" format="fasta" label="Protein sequence database" help=" select fasta data sets(s)"/>
    <param argument="-in_featureXML" type="data" format="featurexml" label="Feature data annotated with identifications (IDMapper)" help=" select featurexml data sets(s)"/>
    <param argument="-mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help=""/>
    <param argument="-rt_tolerance_s" type="float" value="30.0" label="Tolerance window around feature rt for XIC extraction" help=""/>
    <param argument="-intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help=""/>
    <param argument="-correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help=""/>
    <param argument="-xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
    <param argument="-decomposition_threshold" type="float" value="0.7" label="Minimum R-squared of decomposition that must be achieved for a peptide to be reported" help=""/>
    <param argument="-weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/>
    <param argument="-plot_extension" type="select" label="Extension used for plots (png|svg|pdf)" help="">
      <option value="png" selected="true">png</option>
      <option value="svg">svg</option>
      <option value="pdf">pdf</option>
      <expand macro="list_string_san" name="plot_extension"/>
    </param>
    <param argument="-qc_output_directory" type="text" optional="true" value="" label="Output directory for the quality report" help="">
      <expand macro="list_string_san" name="qc_output_directory"/>
    </param>
    <param argument="-labeling_element" type="select" label="Which element (single letter code) is labeled" help="">
      <option value="C" selected="true">C</option>
      <option value="N">N</option>
      <option value="H">H</option>
      <option value="O">O</option>
      <expand macro="list_string_san" name="labeling_element"/>
    </param>
    <param argument="-use_unassigned_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include identifications not assigned to a feature in pattern detection" help=""/>
    <param argument="-use_averagine_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use averagine peptides as model to perform pattern detection on unidentified peptides" help=""/>
    <param argument="-report_natural_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether purely natural peptides are reported in the quality report" help=""/>
    <param argument="-filter_monoisotopic" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help=""/>
    <param argument="-cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grouping" help=""/>
    <expand macro="adv_opts_macro">
      <param argument="-min_correlation_distance_to_averagine" type="float" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/>
      <param argument="-pattern_15N_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
      <param argument="-pattern_13C_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
      <param argument="-pattern_2H_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
      <param argument="-pattern_18O_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
      <param argument="-heatmap_bins" type="integer" value="20" label="Number of RIA bins for heat map generation" help=""/>
      <param argument="-observed_peak_fraction" type="float" value="0.5" label="Fraction of observed/expected peaks" help=""/>
      <param argument="-min_consecutive_isotopes" type="integer" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/>
      <param argument="-score_plot_yaxis_min" type="float" value="0.0" label="The minimum value of the score axis" help="Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
      <param argument="-collect_method" type="select" label="How RIAs are collected" help="">
        <option value="correlation_maximum" selected="true">correlation_maximum</option>
        <option value="decomposition_maximum">decomposition_maximum</option>
        <expand macro="list_string_san" name="collect_method"/>
      </param>
      <param argument="-lowRIA_correlation_threshold" type="float" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="Disable and take correlation_threshold value for negative values"/>
      <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_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"/>
    <data name="out_peptide_centric_csv" label="${tool.name} on ${on_string}: out_peptide_centric_csv" format="csv"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_MetaProSIP_1 -->
    <test expect_num_outputs="3">
      <section name="adv_opts">
        <param name="min_correlation_distance_to_averagine" value="-1.0"/>
        <param name="pattern_15N_TIC_threshold" value="0.95"/>
        <param name="pattern_13C_TIC_threshold" value="0.95"/>
        <param name="pattern_2H_TIC_threshold" value="0.95"/>
        <param name="pattern_18O_TIC_threshold" value="0.95"/>
        <param name="heatmap_bins" value="20"/>
        <param name="observed_peak_fraction" value="0.5"/>
        <param name="min_consecutive_isotopes" value="2"/>
        <param name="score_plot_yaxis_min" value="0.0"/>
        <param name="collect_method" value="correlation_maximum"/>
        <param name="lowRIA_correlation_threshold" value="-1.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in_mzML" value="MetaProSIP_1_input.mzML"/>
      <param name="in_fasta" value="MetaProSIP_1_input.fasta"/>
      <output name="out_csv" value="MetaProSIP_1_output_1.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
      <output name="out_peptide_centric_csv" value="MetaProSIP_1_output_2.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
      <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/>
      <param name="mz_tolerance_ppm" value="10.0"/>
      <param name="rt_tolerance_s" value="30.0"/>
      <param name="intensity_threshold" value="10.0"/>
      <param name="correlation_threshold" value="0.7"/>
      <param name="xic_threshold" value="0.7"/>
      <param name="decomposition_threshold" value="0.7"/>
      <param name="weight_merge_window" value="5.0"/>
      <param name="plot_extension" value="png"/>
      <param name="qc_output_directory" value=""/>
      <param name="labeling_element" value="C"/>
      <param name="use_unassigned_ids" value="false"/>
      <param name="use_averagine_ids" value="false"/>
      <param name="report_natural_peptides" value="false"/>
      <param name="filter_monoisotopic" value="false"/>
      <param name="cluster" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
  </tests>
  <help><![CDATA[Performs proteinSIP on peptide features for elemental flux analysis.


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