annotate RNA_fragment_size.xml @ 63:27e16a30667a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de

<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>
     calculates the fragment size for each gene/transcript
    </description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <version_command><![CDATA[RNA_fragment_size.py --version]]></version_command>
    <command><![CDATA[
        @BAM_SAM_INPUTS@
        RNA_fragment_size.py -i 'input.${extension}' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}'
        ]]>
    </command>
    <inputs>
        <expand macro="bam_param"/>
        <expand macro="refgene_param"/>
        <expand macro="mapq_param"/>
        <param name="fragnum" type="integer" value="3" label="Minimum number of fragments (default: 3)" help="(--frag-num)"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
            <output name="output">
                <assert_contents>
                    <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$"/>
                    <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$"/>
                    <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$"/>
                    <has_line_matching expression="^chr1\t17368\t17436\tNR_106918\t0\t0\t0\t0$"/>
                    <has_line_matching expression="^chr1\t17368\t17436\tNR_107062\t0\t0\t0\t0$"/>
                    <has_line_matching expression="^chr1\t34610\t36081\tNR_026818\t0\t0\t0\t0$"/>
                    <has_line_matching expression="^chr1\t34610\t36081\tNR_026820\t0\t0\t0\t0$"/>
                    <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
RNA_fragment_size.py
++++++++++++++++++++

Calculate fragment size for each gene/transcript. For each transcript, it will
report : 1) Number of fragment that was used to estimate mean, median, std (see
below). 2) mean of fragment size 3) median of fragment size 4) stdev of fragment
size.

Inputs
++++++

Input BAM/SAM file
    Alignment file in BAM/SAM format.

Reference gene model
    Reference gene model in BED format. Must be strandard 12-column BED file.
    [required]

Minimum mapping quality
    Minimum mapping quality for an alignment to be considered as "uniquely
    mapped". default=30

Minimum number of fragments
    Minimum number of fragments. default=3

@ABOUT@

]]>

    </help>
    <expand macro="citations"/>
</tool>