annotate dbbuilder.xml @ 7:a94dc3d469cb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit 7480b93ed88eb017041b16e1181a481f7b3334d3

<tool id="dbbuilder" name="Protein Database Downloader" version="0.2.1">
    <description></description>
    <requirements>
        <requirement type="package">gnu-wget</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error downloading database." />
        <regex match="ERROR" level="fatal" source="stderr" description="Error downloading database." />
    </stdio>
      <!-- TODO: escape quotes. -->
        <!-- Add NCBI and maxquant contaminants. -->
        <!-- http://maxquant.org/contaminants.zip -->
        <!-- ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz-->
    <command>
<![CDATA[
        #if $source.from == "uniprot"
            #set $url = 'http://www.uniprot.org/uniprot/?query=taxonomy:"' + str($source.taxon) + '"' + str($source.set) + str($source.reviewed) + '&force=yes&format=fasta' + str($source.include_isoform)
            #set $type = "direct"
        #elif $source.from == "cRAP"
            ##set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta"
            #set $url = "https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta"
            #set $type = "direct"
        #elif $source.from == "url"
            #set $url = $source.url
            #set $type = "direct"
        #end if
        #if $type =="direct"
            wget -nv '$url' -O '${output_database}'
        #end if
]]>
    </command>
    <inputs>
        <conditional name="source">
            <param name="from" type="select" label="Download from" help="Select database source. cRAP acts as a database for common MS contaminants. UniProtKB is a corss species collection of functional protein databases">
                <option value="uniprot">UniProtKB</option>
                <option value="cRAP">cRAP (contaminants)</option>
                <option value="url">Custom URL</option>
            </param>
            <when value="uniprot">
                <param name="taxon" type="select" format="text" help="select species for protein database">
                    <label>Taxonomy</label>
                    <options from_file="uniprot_taxons.loc">
                        <column name="name" index="0" />
                        <column name="value" index="1" />
                    </options>
                </param>
                <param name="reviewed" type="select" help="UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database- may contain redundant sequences, but there is a higher chance peptides will be identified. UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database- less of a chance peptides will be identified but less sequence redundancy">
                    <option value="+">UniProtKB</option>
                    <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option>
                    <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option>
                    <sanitizer>
                        <valid>
                            <add value="%"/>
                        </valid>
                    </sanitizer>
                </param>
                <param name="set" type="select" label="Proteome Set">
                    <option value="+">Any</option>
                    <option value="+keyword%3a1185" selected="true">Reference Proteome Set</option>
                    <option value="+keyword%3a181">Complete Proteome Set</option>
                    <sanitizer>
                        <valid>
                            <add value="%"/>
                        </valid>
                    </sanitizer>
                </param>
                <param name="include_isoform" type="boolean" truevalue="&amp;include=yes" falsevalue="" label="Include isoform data" help="several different forms of a given protein are incorporated into database" />
            </when>
            <when value="cRAP" />
            <when value="url">
                <param name="url" value="" type="text" label="URL (http, ftp)">
                    <sanitizer>
                        <valid>
                            <add value="%"/>
                        </valid>
                    </sanitizer>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="fasta" name="output_database" label="Protein Database" />
    </outputs>
    <tests>
        <test>
            <param name="from" value="cRAP" />
            <output name="output_database">
                <assert_contents>
                    <has_text text="KKA1_ECOLX" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
**Output**

Creates a FASTA file of specified protein sequences for comparison with experimental MS/MS data in search algorithm. 

**External Links**

_Galaxy-P 101 shows usage Protein Database Downloader tool in the creation of a workflow
.. _Galaxy-P 101: http://msi-galaxy-p.readthedocs.org/en/latest/sections/galaxyp_101.html
_UniProtKB provides additional information about the UniProt Knowledgebase
.. _UniProtKB: http://www.uniprot.org/help/uniprotkb
]]>
    </help>
</tool>