annotate temp.xml @ 16:c613f8c96e6d draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit c734ef937d8ed788fded64ed8455e7fc7b89278c

<tool id ="run_TEMP" name="TEMP" version="0.1.8">
    <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 $__tool_directory__/scripts/TEMP_Insertion.sh
        -x "$minimum_score_difference"
        -i alignment.sorted.bam
        -s $__tool_directory__/scripts
        -r "$consensus_te_seqs"
        -t "$te_locations"
        -m "$mismatches"
        -f "$median_insertsize"
        -c \${GALAXY_SLOTS:-2} &&
        bash $__tool_directory__/scripts/TEMP_Absence.sh
        -x "$minimum_score_difference"
        -i alignment.sorted.bam
        -s $__tool_directory__/scripts
        -r "$te_locations"
        -t "$reference2bit"
        -f "$median_insertsize"
        -c \${GALAXY_SLOTS:-2} &&
        zip archive.zip  *insertion* *excision* *absence* && mv archive.zip $archive &&
        mv alignment.insertion.refined.bp.summary $insertion_summary &&
        mv alignment.absence.refined.bp.summary $absence_summary
    ]]></command>
    <inputs>
        <param format="bam" name="alignment" type="data" label="Alignment bam file"/>
        <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/>
        <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/>
        <param format="bed" name="te_locations" type="data" label="TE Locations bed file"/>
        <param name="median_insertsize" value="" type="integer" label="Median Insert Length"/>
        <param name="mismatches" min="0" max="5" type="integer" value="3" label="Allow this many mismatches when aligning to TEs"/>
        <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum score difference between optimal and suboptimal alignment to consider read uniquely mapped"/>
    </inputs>
    <outputs>
        <data format="bed" type="data" name="insertion_summary" label="${alignment.element_identifier} Insertions" />
        <data format="bed" type="data" name="absence_summary" label="${alignment.element_identifier} Absences" />
        <data format="zip" type="data" name="archive" label="${alignment.element_identifier} Compressed output files" />
    </outputs>
    <tests>
        <test>
            <param name="alignment" value="chr2l_bwa_mem.bam" ftype="bam"/>
            <param name="reference2bit" value="dm6_chr2l.twobit" ftype="twobit"/>
            <param name="consensus_te_seqs" value="test_consensus.fa" ftype="fasta"/>
            <param name="te_locations" value="test_TE_annotation.gff3" ftype="bed"/>
            <param name="median_insertsize" value="500" ftype="integer"/>
            <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
-------------
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


Output files
-------------


For TE insertion analysis there are 14 columns in the summary file::

    Column 1: The chromosome where the detected insertion happens.
    Column 2: The coordinate of the start position of the detected insertion.
    Column 3: The coordinate of the end position of the detected insertion.
    Column 4: The TE family that the detected insertion belongs to.
    Column 5: The direction of the insertion. “Plus” means that the TE is integrated with the plus strand of the genome while “minus” means the TE is integrated with the minus strand.
    Column 6: The class of the insertion. “1p1” means that the detected insertion is supported by reads at both sides. “2p” means the detected insertion is supported by more than 1 read at only 1 side. “Singleton” means the detected insertion is supported by only 1 read at 1 side.
    Column 7: The total number of read pairs that support the detected insertion.
    Column 8: The estimated population frequency of the detected insertion.
    Columns 9 & 10: The coordinate of a junction and the number of the reads supporting it. If the junction is not found column 9 will be the arithmetic mean of the start and end coordinates and column 10 will have the value 0.
    Columns 11 & 12: Same as Columns 9 & 10 except for the junction on the other strand.
    Column 13: The number of reads supporting the detected insertion at the 5’ end of the TE (not including junction spanning reads).
    Column 13: The number of reads supporting the detected insertion at the 3’ end of the TE (not including junction spanning reads).


For TE absence analysis there are 9 columns in the summary file::

    Column 1: The chromosome where the detected absence happens.
    Column 2: The coordinate of the start position of the detected absence.
    Column 3: The coordinate of the end position of the detected absence.
    Column 4: The TE family that the detected insertion belongs to.
    Column 5: Junctions at 5’ of the excised TE. The two numbers are the coordinates of the junctions on the two strands.
    Column 6: Junctions at 3’ of the excised TE. The two numbers are the coordinates of the junctions on the two strands.
    Column 7: The number of reads supporting the absence.
    Column 8: The number of reads supporting the reference (no absence).
    Column 9: Estimated population frequency of the detected absence event.


    ]]> </help>
    <citations>
        <citation type="doi">10.1093/nar/gku323</citation>
    </citations>
</tool>