view minimus2/minimus2.xml @ 0:937ba44abdb7 default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

<tool id="minimus2" name="Minimus2" version='1.0.1'>
<description>Merge two sets of assembled contig sequences</description>
<command interpreter='perl'>minimus2_wrapper.pl -tmpdir $contigs_outfile.extra_files_path $infile1 $infile2 $contigs_outfile $singletons_outfile
#if $prefix1.select == 'y':
-prefix1 $prefix1.prefix
#end if
#if $prefix2.select == 'y':
-prefix2 $prefix2.prefix
#end if
</command>
<inputs>
    <param name="infile1" type="data" format="fasta" label="Contig sequences file 1"/>
    <conditional name='prefix1'>
        <param name='select' type='select' label='Rename contigs in file 1 by adding prefix?'>
            <option value='y'>yes, add prefix</option>
            <option value='n'>no, contig IDs are unique</option>
        </param>
        <when value='y'>
            <param name="prefix" type="text" value="1" label="Prefix for sequences in file 1" />
        </when>
        <when value='n'>
        </when>
    </conditional>
    <param name="infile2" type="data" format="fasta" label="Contig sequences file 2"/>
    <conditional name='prefix2'>
        <param name='select' type='select' label='Rename contigs in file 2 by adding prefix?'>
            <option value='y'>yes, add prefix</option>
            <option value='n'>no, contig IDs are unique</option>
        </param>
        <when value='y'>
            <param name="prefix" type="text" value="2" label="Prefix for sequences in file 2" />
        </when>
        <when value='n'>
        </when>
    </conditional>
</inputs>
<outputs>
    <data name="contigs_outfile" format="fasta" label="contigs" />
    <data name="singletons_outfile" format="fasta" label="singletons" />
</outputs>
<help>
**What it does**

minimus2 is part of the AMOS assembler package, designed for merging one or two sets of contig sequences.

This tool preprocesses the Fasta input files prior to coassembly with minimus2 and separately returns the new contigs
and the sequences which did not co-assemble (singletons).

The input sequences in each dataset must have unique IDs; use of the optional rename with prefix option avoids this.

**Documentation**

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus2
</help>
</tool>