comparison tools/mira4/mira4_mapping.xml @ 9:302d13490b23 draft

Uploaded v0.0.2 preview 1, BAM output

8:2ab1d6f6a8ec

<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.1">
    <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
    <requirements>
        <requirement type="binary">mira</requirement>
        <requirement type="package" version="4.0">MIRA</requirement>
    </requirements>
    <version_command interpreter="python">mira4.py --version</version_command>
    <command interpreter="python">
mira4.py $manifest $out_maf $out_fasta $out_log
    </command>
    <inputs>
        <param name="job_type" type="select" label="Assembly type">
            <option value="genome">Genome</option>
            <option value="est">EST (transcriptome)</option>
        </param>

                   help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
        </repeat>
    </inputs>
    <outputs>
        <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" />
        <data name="out_maf" format="mira" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly" />
        <data name="out_log" format="txt" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping log" />
    </outputs>
    <configfiles>
        <configfile name="manifest">

    </tests>
    <help>

**What it does**

Runs MIRA v4.0 in mapping mode, collects the output, and throws away all the temporary files.

MIRA is an open source assembly tool capable of handling sequence data from
a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent
and also PacBio).

9:302d13490b23

<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.2">
    <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
    <requirements>
        <requirement type="binary">mira</requirement>
        <requirement type="binary">miraconvert</requirement>
        <requirement type="package" version="4.0">MIRA</requirement>
        <requirement type="binary">samtools</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
    </requirements>
    <version_command interpreter="python">mira4.py --version</version_command>
    <command interpreter="python">
mira4.py "$manifest" "$out_maf" "$out_bam" "$out_fasta" "$out_log"
    </command>
    <stdio>
        <!-- Assume anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <inputs>
        <param name="job_type" type="select" label="Assembly type">
            <option value="genome">Genome</option>
            <option value="est">EST (transcriptome)</option>
        </param>

                   help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
        </repeat>
    </inputs>
    <outputs>
        <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" />
        <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)" />
        <data name="out_maf" format="mira" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly" />
        <data name="out_log" format="txt" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping log" />
    </outputs>
    <configfiles>
        <configfile name="manifest">

    </tests>
    <help>

**What it does**

Runs MIRA v4.0 in mapping mode, collects the output, generates a sorted BAM
file, and throws away all the temporary files.

MIRA is an open source assembly tool capable of handling sequence data from
a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent
and also PacBio).