comparison MetaProSIP.xml @ 5:fdb3fbfef4cc draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

4:05f78b9d5874

<?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: [Utilities]-->
<tool id="MetaProSIP" name="MetaProSIP" version="2.2.0.1">
  <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
  <macros>
    <token name="@EXECUTABLE@">MetaProSIP</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements">
      <requirement type="package" version="3.3.1">r-base</requirement>
  </expand>
  <command>MetaProSIP

#if $param_in_mzML:
  -in_mzML $param_in_mzML

  -out_peptide_centric_csv $param_out_peptide_centric_csv
#end if
#if $param_in_featureXML:
  -in_featureXML $param_in_featureXML
#end if

-r_executable 'R'

#if $param_mz_tolerance_ppm:
  -mz_tolerance_ppm $param_mz_tolerance_ppm
#end if
#if $param_rt_tolerance_s:
  -rt_tolerance_s $param_rt_tolerance_s

    <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
    <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
    <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
    <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/>
    <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) 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 name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R^2 of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/>
    <param name="param_weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help="(-weight_merge_window) "/>
    <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) ">
      <option value="png" selected="true">png</option>
      <option value="svg">svg</option>
      <option value="pdf">pdf</option>

    <data name="param_out_peptide_centric_csv" format="tabular"/>
  </outputs>
  <help>Performs proteinSIP on peptide features for elemental flux analysis.


For more information, visit http://www.openms.de/comp/metaprosip/</help>
</tool>

5:fdb3fbfef4cc

<?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: [Utilities]-->
<tool id="MetaProSIP" name="MetaProSIP" version="2.3.0">
  <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
  <macros>
    <token name="@EXECUTABLE@">MetaProSIP</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements">
    <requirement type="package" version="3.4.1">r-base</requirement>
  </expand>
  <command>MetaProSIP

#if $param_in_mzML:
  -in_mzML $param_in_mzML

  -out_peptide_centric_csv $param_out_peptide_centric_csv
#end if
#if $param_in_featureXML:
  -in_featureXML $param_in_featureXML
#end if
#if $param_mz_tolerance_ppm:
  -mz_tolerance_ppm $param_mz_tolerance_ppm
#end if
#if $param_rt_tolerance_s:
  -rt_tolerance_s $param_rt_tolerance_s

    <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
    <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
    <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
    <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/>
    <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) 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 name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R² of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/>
    <param name="param_weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help="(-weight_merge_window) "/>
    <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) ">
      <option value="png" selected="true">png</option>
      <option value="svg">svg</option>
      <option value="pdf">pdf</option>

    <data name="param_out_peptide_centric_csv" format="tabular"/>
  </outputs>
  <help>Performs proteinSIP on peptide features for elemental flux analysis.


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