comparison dbbuilder.xml @ 9:c1b437242fee draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit b1ccd85b9c91cf311f92e6b9999fddd6d2408b20"

8:a85fbebe8b2f

<tool id="dbbuilder" name="Protein Database Downloader" version="0.3.0">
    <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>

            #if str($source.annotation).endswith('.tar.gz'):
                #set $type = "tgz" 
            #elif str($source.annotation).endswith('.zip'):
                #set $type = "zip" 
            #end if 
        #elif $source.from == 'EBI Metagenomics'
            #set $url = 'https://www.ebi.ac.uk/metagenomics/projects/' + str($source.ebi_project) + '/samples/' + str($source.ebi_sample) + '/runs/' + str($source.ebi_run) + '/results/versions/' + str($source.ebi_version) + '/sequences/' + str($source.ebi_annotation) + '/chunks/1'
            #set $type = "gzip"
        #elif $source.from == "url"
            #set $url = $source.url
            #set $type = $source.archive_type
        #end if
        #if $type =="direct"

        <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 cross species collection of functional protein databases">
                <option value="uniprot">UniProtKB</option>
                <option value="cRAP">cRAP (contaminants)</option>
                <option value="HMP">Human Microbiome Project body sites</option>
                <option value="EBI Metagenomics">EBI Metagenomics</option>
                <option value="HOMD">Human Oral Microbiome Database (HOMD)</option>
                <option value="url">Custom URL</option>
            </param>
            <when value="uniprot">
                <param name="taxon" type="select" format="text" help="select species for protein database">

                    <option value="Gastrointestinal_tract">HMP Gastro-intestinal tract</option>
                    <option value="Oral">HMP Oral</option>
                    <option value="Skin">HMP Skin</option>
                    <option value="Urogenital_tract">HMP urogenital Tract</option>
                </param>
            </when>
            <when value="EBI Metagenomics">
                <param name="ebi_project" value="" type="text" label="EBI Metagenomics Project (e.g. DRP003095)">
                <help><![CDATA[
Look up EBI Metagenomics at https://www.ebi.ac.uk/metagenomics/search 
                ]]></help>
                </param>
                <param name="ebi_sample" value="" type="text" label="EBI Metagenomics Sample (e.g. DRS029200)">
                </param>
                <param name="ebi_run" value="" type="text" label="EBI Metagenomics Run (e.g. DRR033743)">
                </param>
                <param name="ebi_version" value="" type="text" label="EBI Metagenomics Pipeline Version (e.g. 3.0)">
                </param>
                <param name="ebi_annotation" type="boolean" label="With Annotation" checked="true" 
                      truevalue="PredictedCDSWithAnnotation" falsevalue="PredictedCDSWithioutAnnotation"/>
                      
            </when>
            <when value="HOMD">
                <param name="annotation" type="select" label="Human Oral Microbiome Proteome">
                    <option value="oral_microbiome_dynamic.aa.zip">HOMD with dynamic annotation</option>
                    <option value="oral_microbiome.aa.tar.gz">HOMD with static annotation</option>

                <assert_contents>
                    <has_text text="KKA1_ECOLX" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="from" value="EBI Metagenomics" />
            <param name="ebi_project" value="DRP003095" />
            <param name="ebi_sample" value="DRS029200" />
            <param name="ebi_run" value="DRR033743" />
            <param name="ebi_version" value="3.0" />
            <output name="output_database">
                <assert_contents>
                    <has_text text="DRR033743" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
**Output**

**Additional Protein Fasta URLs**

  *HUMAN GUT METAPROTEOME:*

    * 512MB gzip ftp://public.genomics.org.cn/BGI/gutmeta/UniSet/UniGene.pep.gz
    *  61MB gzip http://www.bork.embl.de/~arumugam/Qin_et_al_2010/frequent_microbe_proteins.fasta.gz


  *MOUSE GUT MICROBIOTA:*

    * 417MB gzip ftp://climb.genomics.cn/pub/10.5524/100001_101000/100114/Genecatalog/184sample_2.6M.GeneSet.pep.gz
    * See: http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP


]]>
    </help>

9:c1b437242fee

<tool id="dbbuilder" name="Protein Database Downloader" version="0.3.1">
    <description></description>
    <requirements>
        <requirement type="package" version="1.20.1">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>

            #if str($source.annotation).endswith('.tar.gz'):
                #set $type = "tgz" 
            #elif str($source.annotation).endswith('.zip'):
                #set $type = "zip" 
            #end if 
        #elif $source.from == "url"
            #set $url = $source.url
            #set $type = $source.archive_type
        #end if
        #if $type =="direct"

        <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 cross species collection of functional protein databases">
                <option value="uniprot">UniProtKB</option>
                <option value="cRAP">cRAP (contaminants)</option>
                <option value="HMP">Human Microbiome Project body sites</option>
                <option value="HOMD">Human Oral Microbiome Database (HOMD)</option>
                <option value="url">Custom URL</option>
            </param>
            <when value="uniprot">
                <param name="taxon" type="select" format="text" help="select species for protein database">

                    <option value="Gastrointestinal_tract">HMP Gastro-intestinal tract</option>
                    <option value="Oral">HMP Oral</option>
                    <option value="Skin">HMP Skin</option>
                    <option value="Urogenital_tract">HMP urogenital Tract</option>
                </param>
            </when>
            <when value="HOMD">
                <param name="annotation" type="select" label="Human Oral Microbiome Proteome">
                    <option value="oral_microbiome_dynamic.aa.zip">HOMD with dynamic annotation</option>
                    <option value="oral_microbiome.aa.tar.gz">HOMD with static annotation</option>

                <assert_contents>
                    <has_text text="KKA1_ECOLX" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
**Output**

**Additional Protein Fasta URLs**

  *HUMAN GUT METAPROTEOME:*

    *  61MB gzip http://www.bork.embl.de/~arumugam/Qin_et_al_2010/frequent_microbe_proteins.fasta.gz


  *MOUSE GUT MICROBIOTA:*

    * See: http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP


]]>
    </help>