view proteomiqon_joinquantpepionswithproteins.xml @ 0:ecf5a558dc8a draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"

<tool id="proteomiqon_joinquantpepionswithproteins" name="Proteomiqon JoinQuantPepIonsWithProteins" version="@VERSION@" profile="20.05">
    <description>
        combines the results from ProteinInference and PSMBasedQuantification.
    </description>
    <macros>
        <token name="@VERSION@">0.0.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">proteomiqon-joinquantpepionswithproteins</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #import re
        #set quant_basename = $re.sub(r'[^\w ,.\-+]','_',$quantifiedpeptides.element_identifier)
        ln -s '$quantifiedpeptides' '${quant_basename}.quant' &&
        #set prot_basename = $re.sub(r'[^\w ,.\-+]','_',$inferredproteins.element_identifier)
        ln -s '$inferredproteins' '${prot_basename}.prot' &&
        ln -s '$out_quantAndProt' '${quant_basename}.quantAndProt' &&  
        proteomiqon-joinquantpepionswithproteins -i '${quant_basename}.quant' -ii '${prot_basename}.prot' -o './'
    ]]>
    </command>
    <inputs>
        <param name="quantifiedpeptides" type="data" format="tabular" label="Quantified Peptides" help="Specify Quantified Peptides." />
        <param name="inferredproteins" type="data" format="tabular" label="Inferred Proteins" help="Specify Inferred Proteins." />
    </inputs>
    <outputs>
        <data format="tabular" name="out_quantAndProt" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="quantifiedpeptides" value="sample.quant"/>
            <param name="inferredproteins" value="sample.prot"/>
            <output name="out_quantAndProt" file="sample_out.quantAndProt"/>
        </test>
    </tests>
    <help>
    <![CDATA[
What It Does
------------
**Disclaimer** this tool needs the results from ProteinInference and PSMBasedQuantification.

Results from PSMBasedQuantification contain detailed information about the quantification of every peptide, but only basic informations about the protein they 
originated from. This information is obtained during the ProteinInference. This tool takes the results from both tools and combines the qauntification information of
each peptide with the more accurate information about the corresponding protein including its q-value.

Further Reading
---------------
Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html>`_.  
    ]]>
    </help>
</tool>