view tools/ncbi_blast_plus/get_species_taxids.xml @ 33:d999e774072a draft

Fix for get_species_taxids

<tool id="get_species_taxids" name="NCBI get species taxids" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description></description>
    <macros>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="preamble"/>
    <command detect_errors="aggressive"><![CDATA[
#if $type_cond.type_sel == 'names'
    #for name in $type_cond.names.split(',')
        taxid=\$(get_species_taxids.sh -n '$name' | grep Taxid | sed 's/Taxid\s*:\s*//') &&
        if [ -z "\$taxid" ]; then
            >&2 echo "could not find taxid for $name" && exit 1;
        else
            echo " $name -> \$taxid";
        fi &&
        get_species_taxids.sh -t "\$taxid" >> species_ids.txt &&
    #end for
#else
    #for taxid in $type_cond.ids.split(',')
       get_species_taxids.sh -t "$taxid" >> species_ids.txt &&
    #end for
#end if
sort -n -u  species_ids.txt > '$output'
    ]]></command>
    <inputs>
        <conditional name="type_cond">
            <param name="type_sel" type="select" label="Get taxids by">
                <option value="names">Taxon names</option>
                <option value="ids">Taxon ids</option>
            </param>
            <when value="names">
                <param name="names" type="text" label="Taxon names" help="comma separated">
                    <validator type="regex" message="Enter a comma separated list of taxon names">[a-zA-Z ,]+$</validator>
                </param>
            </when>
            <when value="ids">
                <param name="ids" type="text" label="Taxon ids" help="comma separated">
                    <validator type="regex" message="Enter a comma separated list of taxids">[0-9,]+$</validator>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="type_cond|type_sel" value="names"/>
            <param name="type_cond|names" value="Enterobacterales"/>
            <output name="output" ftype="txt">
                <assert_contents>
                    <has_line line="9"/>
                    <has_line line="2791989"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="type_cond|type_sel" value="ids"/>
            <param name="type_cond|ids" value="91347"/>
            <output name="output" ftype="txt">
                <assert_contents>
                    <has_line line="9"/>
                    <has_line line="2791989"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="type_cond|type_sel" value="names"/>
            <param name="type_cond|names" value="Enterobacterales,Hominidae"/>
            <output name="output" ftype="txt">
                <assert_contents>
                    <has_line line="9"/>
                    <has_line line="9606"/>
                    <has_line line="2791989"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="type_cond|type_sel" value="ids"/>
            <param name="type_cond|ids" value="91347,9604"/>
            <output name="output" ftype="txt">
                <assert_contents>
                    <has_line line="9"/>
                    <has_line line="9606"/>
                    <has_line line="2791989"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

**What it does**

Returns a list of species taxids for a taxon. It relies on the get_species_taxids.sh script of the BLAST+ package https://www.ncbi.nlm.nih.gov/books/NBK546209/

-------

**References**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:

@REFERENCES@
    </help>
    <expand macro="blast_citations"/>
</tool>