comparison uniprotxml_downloader.xml @ 4:12692567c7f9 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"

3:1a5690a5eedc

<tool id="uniprotxml_downloader" name="UniProt" version="2.1.0">
    <description>download proteome as XML or fasta</description>
    <requirements>
        <requirement type="package" version="2.7">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.input_choice == 'common':
--taxon $taxid.organism
#if $taxid.reviewed:
--reviewed=$taxid.reviewed
#end if
#elif $taxid.input_choice == 'taxids':
#for $id in $taxid.taxons.split(','):
-t "$id"
#end for
#elif $taxid.input_choice == 'history':
--input="${taxid.taxon_file}"
--column=#echo int(str($taxid.column)) - 1#
#end if
--format=$format
--output="${proteome}"
]]>
    </command>
    <inputs>
        <conditional name="taxid">
            <param name="input_choice" type="select" label="Select">
                <option value="common">A Common Organism</option>
                <option value="taxids">By Organism IDs</option>
                <option value="history">A history dataset with an Organism Taxonomy Name column</option>
            </param>
            <when value="common">
                <param name="organism" type="select" label="Common Organisms"
                       help="select species for protein database">
                    <options from_file="uniprot_taxons.loc">

                       help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/">
                    <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator>
                </param>
            </when>
            <when value="history">
                <param name="taxon_file" type="data" format="tabular" label="Dataset with Taxon Name column"/>
                <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon name"/>
            </when>
        </conditional>
        <param name="format" type="select" label="uniprot output format">
            <option value="xml">xml</option>
            <option value="fasta">fasta</option>

                    <has_text text="Shi470" />
                    <has_text text="PeCan4" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
**UniProt Downloader**

4:12692567c7f9

<tool id="uniprotxml_downloader" name="UniProt" version="2.2.0" profile="21.01">
    <description>download proteome as XML or fasta</description>
    <requirements>
        <requirement type="package" version="2.25.1">requests</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error downloading proteome." />
    </stdio>
    <command>
<![CDATA[
python '$__tool_directory__/uniprotxml_downloader.py'
#if $taxid.input_choice == 'common':
    --taxon $taxid.organism
    #if $taxid.reviewed:
        --reviewed=$taxid.reviewed
    #end if
#elif $taxid.input_choice == 'taxids':
    #for $id in $taxid.taxons.split(','):
        -t '$id'
    #end for
#elif $taxid.input_choice == 'history':
    --input='${taxid.taxon_file}'
    --column=#echo int(str($taxid.column)) - 1#
#end if
--format $format
--output '${proteome}'
]]>
    </command>
    <inputs>
        <conditional name="taxid">
            <param name="input_choice" type="select" label="Select">
                <option value="common">A Common Organism</option>
                <option value="taxids">A manually entered list of Taxon IDs or names</option>
                <option value="history">A history dataset with a column containing Taxon IDs or names</option>
            </param>
            <when value="common">
                <param name="organism" type="select" label="Common Organisms"
                       help="select species for protein database">
                    <options from_file="uniprot_taxons.loc">

                       help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/">
                    <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator>
                </param>
            </when>
            <when value="history">
                <param name="taxon_file" type="data" format="tabular,txt" label="Dataset (tab separated) with Taxon ID/Name column"/>
                <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon ID/name"/>
            </when>
        </conditional>
        <param name="format" type="select" label="uniprot output format">
            <option value="xml">xml</option>
            <option value="fasta">fasta</option>

                    <has_text text="Shi470" />
                    <has_text text="PeCan4" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_choice" value="history"/>
            <param name="taxon_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/>
            <param name="column" value="2"/>
            <param name="format" value="fasta"/>
            <output name="proteome">
                <assert_contents>
                    <has_text text="Shi470" />
                    <has_text text="PeCan4" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
**UniProt Downloader**