comparison uniprotxml_downloader.xml @ 1:fc8c4bd28681 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6

0:0bd2688166a5

<tool id="uniprotxml_downloader" name="UniProtXML Download" version="1.0.0">
    <description>proteome</description>
    <requirements>
        <requirement type="binary">wget</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error downloading proteome." />
    </stdio>
    <command interpreter="python">
<![CDATA[
uniprotxml_downloader.py -v 
#if $taxid.choice == 'common':
--taxon $taxid.organism
#if $taxid.reviewed:
--reviewed=$taxid.reviewed
#end if
#else:
#for id in $taxid.taxons.split(','):
-t $id
#end for
#end if
--output="${proteome}"
]]>
    </command>
    <inputs>
        <conditional name="taxid">
            <param name="choice" type="select" label="Select">

    <outputs>
        <data format="uniprotxml" name="proteome" label="UniProtXML" />
    </outputs>
    <tests>
        <test>
            <param name="taxons" value="1566990"/>
            <output name="uniprotxml">
                <assert_contents>
                    <has_text text="&lt;/uniprot&gt;" />
                </assert_contents>

1:fc8c4bd28681

<tool id="uniprotxml_downloader" name="UniProtXML Download" version="1.0.1">
    <description>proteome</description>
    <requirements>
        <requirement type="package" version="2.7.12">python</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error downloading proteome." />
    </stdio>
    <command>
<![CDATA[
    python '$__tool_directory__/uniprotxml_downloader.py'
        -v 
        #if $taxid.choice == 'common':
            --taxon '$taxid.organism'
        #if $taxid.reviewed:
            --reviewed=$taxid.reviewed
        #end if
        #else:
        #for id in $taxid.taxons.split(','):
            -t $id
        #end for
        #end if
            --output="${proteome}"
]]>
    </command>
    <inputs>
        <conditional name="taxid">
            <param name="choice" type="select" label="Select">

    <outputs>
        <data format="uniprotxml" name="proteome" label="UniProtXML" />
    </outputs>
    <tests>
        <test>
            <param name="choice" value="taxids"/>
            <param name="taxons" value="1566990"/>
            <output name="uniprotxml">
                <assert_contents>
                    <has_text text="&lt;/uniprot&gt;" />
                </assert_contents>