comparison diamond_makedb.xml @ 6:64be1ac21109 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1

5:3c6b132b154a

    <expand macro="stdio" />
    <expand macro="version_command" />

    <command>
    <!-- DB has two files, *.dmnd and *.tx -->
<![CDATA[
    diamond makedb
        --threads "\${GALAXY_SLOTS:-12}"
        --in '$infile'
        --db ./database
]]>
    </command>

    <inputs>
        <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
    </inputs>

    <outputs>
        <data format="dmnd" name="outfile" from_work_dir="database.dmnd" label="${tool.name} on ${on_string}"/>
    </outputs>

    <tests>
        <test>
            <param name="infile" value="db.fasta" ftype="fasta"/>
            <output name="outfile" value="db.dmnd"/>
        </test>
    </tests>

    <help>
<![CDATA[

times faster than BLASTX, finding more than 94% of all matches.

.. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/


]]>
    </help>

    <expand macro="citations" />
</tool>

6:64be1ac21109

    <expand macro="stdio" />
    <expand macro="version_command" />

    <command>
    <!-- DB has two files, *.dmnd and *.tx -->
    <![CDATA[
    diamond makedb
        --threads "\${GALAXY_SLOTS:-12}"
        --in '$infile'
        --db ./database

      #if str($tax_cond.tax_select) == 'yes':
        --taxonmap '$tax_cond.taxonmap'
        --taxonnodes '$tax_cond.taxonnodes'
      #end if
    ]]>
    </command>

    <inputs>
      <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
      <conditional name="tax_cond">
        <param name="tax_select" type="select" label="Add taxonomic data?" help="Needs to be supplied in order to provide taxonomy features of the aligner">
          <option value="yes">Yes</option>
          <option value="no" selected="true">No</option>
        </param>
        <when value="yes">
          <param argument="--taxonmap" type="data" format="tabular" label="protein accession to taxid mapping file" help="" />
          <param argument="--taxonnodes" type="data" format="tabular" label="taxonomy nodes.dmp from NCBI" help="" />
        </when>
        <when value="no"/>
      </conditional>
    </inputs>

    <outputs>
        <data format="dmnd" name="outfile" from_work_dir="database.dmnd" label="${tool.name} on ${on_string}"/>
    </outputs>

    <tests>
        <test>
            <param name="infile" value="db.fasta" ftype="fasta"/>
            <output name="outfile" value="db.dmnd" compare="sim_size" delta="2"/>
        </test>
        <test>
            <param name="infile" value="db.fasta" ftype="fasta"/>
            <conditional name="tax_cond">
                <param name="tax_select" value="yes"/>
                <param name="taxonmap" ftype="tabular" value="prot.accession2taxid" />
                <param name="taxonnodes" ftype="tabular" value="nodes.dmp" />
            </conditional>
            <output name="outfile" value="db-wtax.dmnd" compare="sim_size" delta="2"/>
        </test>
    </tests>

    <help>
<![CDATA[

times faster than BLASTX, finding more than 94% of all matches.

.. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/


- taxonmap: Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz

- taxonnodes: Path to the nodes.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
]]>
    </help>

    <expand macro="citations" />
</tool>