comparison mz_to_sqlite.xml @ 2:8df9fe030d68 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 2c0016faa867da59ca020587f3b704e70e16c7ca-dirty

1:77389cf7ff62

<tool id="mz_to_sqlite" name="mz to sqlite" version="1.0.0">
    <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description>
    <requirements>
      <requirement type="package" version="1.0.0">mztosqlite</requirement>
    </requirements>
   <stdio>
       <exit_code range="1:"  level="fatal" description="Error Running mz_to_sqlite" />
   </stdio>
    <command>

]]>
    </command>
    <inputs>
        <param name="mzinputs" type="data" format="mzid" multiple="true" optional="true" label="Proteomics Identification files"/>
        <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/>
        <param name="searchdbs" type="data" format="fasta" multiple="true" optional="true" label="Proteomics Search Database Fasta"
               help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/>
    </inputs>
    <outputs>
        <data format="mz.sqlite" name="mzsqlite" label="${tool.name} on ${on_string}"/>
    </outputs>

2:8df9fe030d68

<tool id="mz_to_sqlite" name="mz to sqlite" version="1.2.0">
    <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description>
    <requirements>
      <requirement type="package" version="1.2.0">mztosqlite</requirement>
    </requirements>
   <stdio>
       <exit_code range="1:"  level="fatal" description="Error Running mz_to_sqlite" />
   </stdio>
    <command>

]]>
    </command>
    <inputs>
        <param name="mzinputs" type="data" format="mzid" multiple="true" optional="true" label="Proteomics Identification files"/>
        <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/>
        <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta"
               help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/>
    </inputs>
    <outputs>
        <data format="mz.sqlite" name="mzsqlite" label="${tool.name} on ${on_string}"/>
    </outputs>