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

Fix for get_species_taxids

32:a52d2d93e595

    </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://') &&
        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>

33:d999e774072a

    </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>