comparison temp.xml @ 15:65ae84fc6689 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 7e0a7a19ee51f12bdcdfe84f3de67530a8990de9

14:bc39ae53be03

<tool id ="run_TEMP" name="TEMP" version=" 0.1.5">
    <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>

        <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 500 -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 $absence_summary
    ]]></command>
    <inputs>
        <param format="bam" name="alignment" type="data" label="Alignment bam file"/>
        <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/>
        <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/>
        <param format="bed" name="te_locations" type="data" label="TE Locations bed file"/>
        <param format="txt" name="median_insertsize" type="data" label="Median Insert Length"/>
        <param name="mismatches" min="0" max="5" type="integer" value="3" label="Allow this many mismatches when aligning to TEs"/>
        <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum score difference between optimal and suboptimal alignment to consider read uniquely mapped"></param>
    </inputs>
    <outputs>
        <data format="bed" type="data" name="insertion_summary" label="${alignment.element_identifier} Insertion summary file" />
        <data format="bed" type="data" name="absence_summary" label="${alignment.element_identifier} Absence summary file" />
        <data format="zip" type="data" name="archive" label="${alignment.element_identifier} Compressed output files" />

        <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="median_insert_size" ftype="txt"/>
            <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.

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

15:65ae84fc6689

<tool id ="run_TEMP" name="TEMP" version="0.1.7">
    <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>

        <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} Insertion summary file" />
        <data format="bed" type="data" name="absence_summary" label="${alignment.element_identifier} Absence summary file" />
        <data format="zip" type="data" name="archive" label="${alignment.element_identifier} Compressed output files" />

        <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
-------------