comparison bam_readtagger.xml @ 20:03415763c62c draft

planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty

19:97c1b92dbd28

<tool id="bam_readtagger" name="Tag alignment files" version="0.3.13">
    <description>from multiple bam files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="0.3.13">readtagger</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        readtagger -t '$tag_file' -a
        #for $element in $alignment_series
            '$element.annotate_with':$element.r_tag:$element.m_tag

                <param name="r_tag" value="A"/>
                <param name="m_tag" value="B"/>
            </repeat>
            <param name="discarded" value="True"/>
            <param name="verified" value="True"/>
            <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="5"/>
            <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="5"/>
            <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="5"/>
        </test>
        <test> <!-- test that a single read originating from a pasteurianus is annotated in pasteurianus.bam as having homology with dm6, but marked as discarded (should end in discarded bam file) -->
            <param name="tag_file" value="pasteurianus.bam" ftype="bam"/>
            <repeat name="alignment_series">
                <param name="annotate_with" value="dm6.bam" ftype="bam"/>
                <param name="r_tag" value="A"/>
                <param name="m_tag" value="B"/>
            </repeat>
            <param name="discarded" value="True"/>
            <param name="verified" value="True"/>
            <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="5" />
            <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="5"/>
            <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="5"/>
        </test>
        <test> <!-- test that a pair with homology to a TE insertion is discarded, because it is a proper pair -->
            <param name="tag_file" value="proper_pair_discard.bam" ftype="bam"/>
            <repeat name="alignment_series">
                <param name="annotate_with" value="proper_pair_discard_fbti.bam" ftype="bam"/>

            </repeat>
            <param name="discarded" value="True"/>
            <param name="keep_suboptimal" value="True"/>
            <param name="discard_proper_pairs" value="True"/>
            <param name="verified" value="True"/>
            <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="5" />
            <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="5"/>
            <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="5"/>
        </test>
    </tests>
    <help><![CDATA[
.. code-block::

20:03415763c62c

<tool id="bam_readtagger" name="Tag alignment files" version="0.3.14">
    <description>from multiple bam files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="0.3.14">readtagger</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        readtagger -t '$tag_file' -a
        #for $element in $alignment_series
            '$element.annotate_with':$element.r_tag:$element.m_tag

                <param name="r_tag" value="A"/>
                <param name="m_tag" value="B"/>
            </repeat>
            <param name="discarded" value="True"/>
            <param name="verified" value="True"/>
            <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="7"/>
            <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="7"/>
            <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="7"/>
        </test>
        <test> <!-- test that a single read originating from a pasteurianus is annotated in pasteurianus.bam as having homology with dm6, but marked as discarded (should end in discarded bam file) -->
            <param name="tag_file" value="pasteurianus.bam" ftype="bam"/>
            <repeat name="alignment_series">
                <param name="annotate_with" value="dm6.bam" ftype="bam"/>
                <param name="r_tag" value="A"/>
                <param name="m_tag" value="B"/>
            </repeat>
            <param name="discarded" value="True"/>
            <param name="verified" value="True"/>
            <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="7" />
            <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="7"/>
            <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="7"/>
        </test>
        <test> <!-- test that a pair with homology to a TE insertion is discarded, because it is a proper pair -->
            <param name="tag_file" value="proper_pair_discard.bam" ftype="bam"/>
            <repeat name="alignment_series">
                <param name="annotate_with" value="proper_pair_discard_fbti.bam" ftype="bam"/>

            </repeat>
            <param name="discarded" value="True"/>
            <param name="keep_suboptimal" value="True"/>
            <param name="discard_proper_pairs" value="True"/>
            <param name="verified" value="True"/>
            <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="7" />
            <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="7"/>
            <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="7"/>
        </test>
    </tests>
    <help><![CDATA[
.. code-block::