comparison MetaProSIP.xml @ 6:96cc79adfadb draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb

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
#end if
#if $param_in_fasta:

    "$param_plot_extension"
  #else
    $param_plot_extension
  #end if
#end if
#if $param_qc_output_directory:
  -qc_output_directory     "$param_qc_output_directory"
#end if
#if $param_labeling_element:
  -labeling_element
  #if " " in str($param_labeling_element):
    "$param_labeling_element"

#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
    <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
    <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
    <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>

    <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>
    </param>
    <param name="param_qc_output_directory" type="text" size="30" label="Output directory for the quality report" help="(-qc_output_directory) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_labeling_element" display="radio" type="select" optional="False" value="C" label="Which element (single letter code) is labeled" help="(-labeling_element) ">
      <option value="C" selected="true">C</option>
      <option value="N">N</option>
      <option value="H">H</option>

      <param name="param_lowRIA_correlation_threshold" type="float" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="(-lowRIA_correlation_threshold) Disable and take correlation_threshold value for negative values"/>
      <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_csv" format="tabular"/>
    <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>

6:96cc79adfadb

<?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="2.3.1">
  <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
  <macros>
    <token name="@EXECUTABLE@">MetaProSIP</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements">
    <requirement type="package" version="3.4.1">r-base</requirement>
    <requirement type="package" version="3.0.1">r-gplots</requirement>
  </expand>
  <expand macro="stdio"/>
  <command><![CDATA[
MetaProSIP

#if $param_in_mzML:
  -in_mzML $param_in_mzML
#end if
#if $param_in_fasta:

    "$param_plot_extension"
  #else
    $param_plot_extension
  #end if
#end if
#if $param_plot_extension == 'pdf':
  -qc_output_directory images
#else
  -qc_output_directory '${html_file.files_path}'
#end if
#if $param_labeling_element:
  -labeling_element
  #if " " in str($param_labeling_element):
    "$param_labeling_element"

#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
-threads "\${GALAXY_SLOTS:-1}"

## remove urls and paths (keeping the file name basename)
&& sed -i -e 's/file:\/\/[^[:space:]]\+\///g; s/\/[^[:space:]]\+\///g' $param_out_csv 

## get html file (should be only one [?])
#if $param_plot_extension != 'pdf':
  && cp '${html_file.files_path}'/*\.html output.html
#end if
 ]]></command>
  <inputs>
    <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
    <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
    <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
    <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>

    <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>
    </param>
    <param name="param_labeling_element" display="radio" type="select" optional="False" value="C" label="Which element (single letter code) is labeled" help="(-labeling_element) ">
      <option value="C" selected="true">C</option>
      <option value="N">N</option>
      <option value="H">H</option>

      <param name="param_lowRIA_correlation_threshold" type="float" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="(-lowRIA_correlation_threshold) Disable and take correlation_threshold value for negative values"/>
      <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_csv" format="tabular" label="${tool.name} on ${on_string}: tabular"/>
    <data name="param_out_peptide_centric_csv" format="tabular" label="${tool.name} on ${on_string}: peptide centric tabular"/>
    <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Webpage">
      <filter>param_plot_extension == 'png' or param_plot_extension == 'svg'</filter>
    </data>
    <collection name="images" type="list" label="${tool.name} on ${on_string}: images">
      <filter>param_plot_extension == 'pdf'</filter>
      <discover_datasets pattern="__name_and_ext__" directory="images" />
    </collection>
  </outputs>
  <tests>
    <test>
      <param name="param_in_mzML" value="MetaProSIP_1_input.mzML"/>
      <param name="param_in_fasta" value="MetaProSIP_1_input.fasta"/>
      <param name="param_in_featureXML" value="MetaProSIP_1_input.featureXML"/>
      <output name="param_out_csv" file="MetaProSIP_1_output_1.csv" />
      <output name="param_out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" />
    </test>
  </tests>
  <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>
<expand macro="references"/>
</tool>