annotate temp.xml @ 10:3200a0299230 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit debe4684eaa00ffcae3c79e7581fdbe41da91d5d

<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.2">
    <description></description>
    <requirements>
        <!-- The following are classical toolshed packages and should be removed
        once conda is deemed stable-->
        <requirement type="package" version="1.6.922">bioperl</requirement>
        <requirement type="package" version="0.7.12">bwa</requirement>
        <requirement type="package" version="2.24">bedtools</requirement>
        <!-- end of toolshed package definitions -->
        <requirement type="package" version="1.6.924">perl-bioperl</requirement>
        <requirement type="package" version="0.7.13">bwa</requirement>
        <requirement type="package" version="2.25.0">bedtools</requirement>
        <requirement type="package" version="324">ucsc-twobittofa</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[

        ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai &&
        ln -f -s "$alignment" alignment.sorted.bam &&
        bash $__tool_directory__/scripts/TEMP_Insertion.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} &&
        bash $__tool_directory__/scripts/TEMP_Absence.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
        mv alignment.insertion.bp.bed $insertion_bed &&
        mv alignment.insertion.refined.bp $insertion_bed_refined &&
        mv alignment.insertion.refined.bp.summary $insertion_summary &&
        mv alignment.absence.refined.bp.summary $absence_summary &&
        zip archive.zip  *insertion* *excision* *absence* &&
        mv archive.zip $archive
    ]]></command>
    <inputs>
        <param format="bam" name="alignment" type="data" label="Alignment bam file"/>
        <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/>
        <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/>
        <param format="bed" name="bed_te_locations" type="data" label="TE Locations bed file"/>
        <!--
        <param format="tabular" name="te_families" type="data" label="TE Families"/>
        <param format="gff" name="gff_te_locations" type="data" label="Reference TE insertion Locations with Family ID names GFF file"/>
        -->
        <param format="txt" name="median_insertsize" type="data" label="Median Insert Length"/>
    </inputs>
    <outputs>
        <data format="bed" type="data" name="insertion_bed" label="Insertion BED file" />
        <data format="bed" type="data" name="insertion_bed_refined" label="Insertion BED file (refined)" />
        <data format="bed" type="data" name="insertion_summary" label="Insertion summary file" />
        <data format="bed" type="data" name="absence_summary" label="Absence summary file" />
        <data format="zip" type="data" name="archive" label="Compressed output files" />
    </outputs>
    <tests>
        <test>
            <param name="alignment" value="test_chromosome.sorted.bam" ftype="bam"/>
            <param name="reference2bit" value="dm3_chr2L.2bit" ftype="twobit"/>
            <param name="consensus_te_seqs" value="test_consensus.fa" ftype="fasta"/>
            <param name="bed_te_locations" value="test_TE_annotation.bed" ftype="bed"/>
            <output name="insertion_bed" file="test_chromosome.insertion.bp.bed" ftype="bed" />
            <output name="insertion_bed_refined" file="test_chromosome.insertion.refined.bp" ftype="bed"/>
            <output name="insertion_summary" file="test_chromosome.insertion.refined.bp.summary" ftype="bed"/>
            <output name="absence_summary" file="test_chromosome.absence.refined.bp.summary" ftype="bed"/>
        </test>
    </tests>
    <help> <![CDATA[


TEMP is a software package for detecting transposable elements (TEs)  insertions and absences from pooled high-throughput sequencing data

Current version v1.04

Author: Jiali Zhuang ([e-mail]) and Jie Wang ([e-mail]) Weng Lab, University of Massachusetts Medical School, Worcester, MA, USA

For TE insertion analysis run TEMP_Insertion.sh in script.
For TE absence analysis run TEMP_Absence.sh in script.


    ]]> </help>
</tool>