view SequenceCoverageCalculator.xml @ 7:e733f018e04c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

<?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="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="2.3.0+galaxy1">
  <description>Prints information about idXML files.</description>
  <macros>
    <token name="@EXECUTABLE@">SequenceCoverageCalculator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="aggressive"><![CDATA[SequenceCoverageCalculator
#if $param_in_database:
  -in_database '$param_in_database'
#end if
#if $param_in_peptides:
  -in_peptides '$param_in_peptides'
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if

## fix output (https://github.com/OpenMS/OpenMS/issues/3605)
## - add header
## - remove reformat data
## - remove summary info
## - print summary info to stdout
| sed '1i#protein\tcoverage%\t#unique hits' 
| sed 's/^\(.*\)(coverage%, #unique hits): \([0-9.]\+\)%, \([0-9]\+\)/\1\t\2\t\3/'
| tee tmpout 
| egrep -v  "^Average coverage|^Average number|^Number of|^SequenceCoverageCalculator took" > '$param_out'
## 
&& cat tmpout | egrep "^Average coverage|^Average number|^Number of|^SequenceCoverageCalculator took"
]]></command>
  <inputs>
    <param name="param_in_database" type="data" format="fasta" optional="False" label="input file containing the database in FASTA format" help="(-in_database) "/>
    <param name="param_in_peptides" type="data" format="idxml" optional="False" label="input file containing the identified peptides" help="(-in_peptides) "/>
    <expand macro="advanced_options">
      <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" format="tabular"/>
  </outputs>
  <tests>
	  <test>
    <param name="param_in_database" ftype="fasta" value="OpenPepXL_input.fasta"/>
    <!-- generated with: IDFilter -best:strict -in ~/projects/OpenMS/src/tests/topp/OpenPepXL_output.idXML -out SequenceCoverageCalculator.idXML-->
    <param name="param_in_peptides" ftype="idxml" value="SequenceCoverageCalculator.idXML" />
    <output name="param_out" file="SequenceCoverageCalculator.tsv" ftype="tabular" />
    </test>
  </tests>
  <help>Prints information about idXML files.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SequenceCoverageCalculator.html</help>
  <expand macro="references"/>
</tool>