comparison infer_experiment.xml @ 51:09846d5169fa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83

50:f242ee103277

<tool id="rseqc_infer_experiment" name="Infer Experiment" version="2.4galaxy1">
    <description>speculates how RNA-seq were configured</description>

    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <requirements>
        <expand macro="requirement_package_numpy" />
        <expand macro="requirement_package_rseqc" />
    </requirements>

    <expand macro="stdio" />

    <version_command><![CDATA[infer_experiment.py --version]]></version_command>

    <command><![CDATA[
        infer_experiment.py -i $input -r $refgene
            --sample-size $sample_size
            --mapq $mapq
            > $output
            ]]>
    </command>

    <inputs>
        <param name="input" type="data" format="bam,sam" label="Input BAM/SAM file" help="(--input-file)"/>
        <param name="refgene" type="data" format="bed" label="Reference gene model in bed format" help="(--refgene)" />
        <param name="sample_size" type="integer" label="Number of reads sampled from SAM/BAM file (default = 200000)" value="200000" help="(--sample-size)"/>
        <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" />
    </inputs>

    <outputs>
        <data format="txt" name="output" />
    </outputs>

    Fraction of reads explained by other combinations: 0.0000
    =========================================================

*Conclusion*: This is single-end, strand specific RNA-seq data. Strandness of reads are concordant with strandness of reference gene.


-----

About RSeQC
+++++++++++

The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.

The RSeQC package is licensed under the GNU GPL v3 license.

.. image:: http://rseqc.sourceforge.net/_static/logo.png

.. _RSeQC: http://rseqc.sourceforge.net/

]]>
    </help>

    <expand macro="citations" />

51:09846d5169fa

<tool id="rseqc_infer_experiment" name="Infer Experiment" version="@WRAPPER_VERSION@">
    <description>speculates how RNA-seq were configured</description>

    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <expand macro="stdio" />

    <version_command><![CDATA[infer_experiment.py --version]]></version_command>

    <command><![CDATA[
        infer_experiment.py -i '${input}' -r '${refgene}'
            --sample-size ${sample_size}
            --mapq ${mapq}
            > '${output}'
            ]]>
    </command>

    <inputs>
        <expand macro="bam_param" />
        <expand macro="refgene_param" />
        <expand macro="sample_size_param" />
        <expand macro="mapq_param" />
    </inputs>

    <outputs>
        <data format="txt" name="output" />
    </outputs>

    Fraction of reads explained by other combinations: 0.0000
    =========================================================

*Conclusion*: This is single-end, strand specific RNA-seq data. Strandness of reads are concordant with strandness of reference gene.

@ABOUT@

]]>
    </help>

    <expand macro="citations" />