comparison alignment.xml @ 2:f29e21388219 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2

1:8c4e2933a17a

<tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.0">
    <description></description>
    <macros>
        <import>vsearch_macros.xml</import>
    </macros>
    <expand macro="requirements" />

    <command>
<![CDATA[
    vsearch
        @GENERAL@
        $acceptall
        --id $id
        --iddef $iddef
        --allpairs_global "$infile"
        --alnout $outfile
        --query_cov $query_cov
        @USERFIELDS@
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--allpairs_global)" />

  --alnout FILENAME           filename for human-readable alignment output
  --acceptall                 output all pairwise alignments

@EXTERNAL_DOCUMENTATION@

-------

@REFERENCES@


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

2:f29e21388219

<tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.1">
    <description></description>
    <macros>
        <import>vsearch_macros.xml</import>
    </macros>
    <expand macro="requirements" />

    <command>
<![CDATA[
    vsearch
        @GENERAL@
        $acceptall
        --id "${id}"
        --iddef "${iddef}"
        --allpairs_global "${infile}"
        --alnout "${outfile}"
        #if str( $query_cov ):
            --query_cov "${query_cov}"
        #end if
        @USERFIELDS@
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--allpairs_global)" />

  --alnout FILENAME           filename for human-readable alignment output
  --acceptall                 output all pairwise alignments

@EXTERNAL_DOCUMENTATION@


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