comparison tools/mira4_0/mira4_mapping.xml @ 4:1713289d9908 draft default tip

v0.0.11 tweak for use with bioconda dependencies

3:a4f602cc3aa9

<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.9">
    <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="4.0.2">MIRA</requirement>
        <requirement type="binary">samtools</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
    </requirements>
    <stdio>
        <!-- Assume anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command interpreter="python">mira4.py --version</version_command>
    <command interpreter="python">mira4.py
--manifest "$manifest"
#if str($maf_wanted) == "true":
--maf "$out_maf"
#end if
#if str($bam_wanted) == "true":
--bam "$out_bam"
#end if
--fasta "$out_fasta"
--log "$out_log"
    </command>
    <configfiles>
        <configfile name="manifest">
project = MIRA
job = mapping,${job_type},${job_quality}

        </param>
        <!-- TODO? Allow technology type for references? -->
        <!-- TODO? Allow strain settings for reference(s) and reads? -->
        <!-- TODO? Use a repeat to allow for multi-strain references? -->
        <!-- TODO? Add strain to the mapping read groups? -->
        <param name="references" type="data" format="fasta,fastq,mira" multiple="true" required="true" label="Backbone reference file(s)"
               help="Multiple files allowed, for example one FASTA file per chromosome or plasmid." />
        <param name="strain_setup" type="select" label="Strain configuration (reference vs reads)">
            <option value="default">Different strains - mapping reads onto a related reference ('StrainX' vs 'ReferenceStrain')</option>
            <option value="same">Same strain - mapping reads from same reference (all 'StrainX')</option>
        </param>

                        <option value="stlouis">St. Louis scheme (see notes)</option>
                    </param>
                </when>
                <when value="none" /><!-- no further questions -->
            </conditional>
            <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
                   help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
        </repeat>
        <param name="maf_wanted" type="boolean" label="Output mapping in MIRA's own format?" checked="False" />
        <param name="bam_wanted" type="boolean" label="Convert mapping into BAM format?" checked="True" />
    </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)">
            <filter>bam_wanted is True</filter>

4:1713289d9908

<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.11">
    <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
    <requirements>
        <requirement type="package" version="4.0.2">MIRA</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
    </requirements>
    <version_command>
python $__tool_directory__/mira4.py --version
    </version_command>
    <command detect_errors="aggressive">
python $__tool_directory__/mira4.py
--manifest '$manifest'
#if str($maf_wanted) == "true":
--maf '$out_maf'
#end if
#if str($bam_wanted) == "true":
--bam '$out_bam'
#end if
--fasta '$out_fasta'
--log '$out_log'
    </command>
    <configfiles>
        <configfile name="manifest">
project = MIRA
job = mapping,${job_type},${job_quality}

        </param>
        <!-- TODO? Allow technology type for references? -->
        <!-- TODO? Allow strain settings for reference(s) and reads? -->
        <!-- TODO? Use a repeat to allow for multi-strain references? -->
        <!-- TODO? Add strain to the mapping read groups? -->
        <param name="references" type="data" format="fasta,fastq,mira" multiple="true" optional="false" label="Backbone reference file(s)"
               help="Multiple files allowed, for example one FASTA file per chromosome or plasmid." />
        <param name="strain_setup" type="select" label="Strain configuration (reference vs reads)">
            <option value="default">Different strains - mapping reads onto a related reference ('StrainX' vs 'ReferenceStrain')</option>
            <option value="same">Same strain - mapping reads from same reference (all 'StrainX')</option>
        </param>

                        <option value="stlouis">St. Louis scheme (see notes)</option>
                    </param>
                </when>
                <when value="none" /><!-- no further questions -->
            </conditional>
            <param name="filenames" type="data" format="fastq,mira" multiple="true" optional="false" label="Read file(s)"
                   help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
        </repeat>
        <param name="maf_wanted" type="boolean" label="Output mapping in MIRA's own format?" checked="false" />
        <param name="bam_wanted" type="boolean" label="Convert mapping into BAM format?" checked="true" />
    </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)">
            <filter>bam_wanted is True</filter>