comparison tin.xml @ 63:27e16a30667a draft default tip

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

62:473382134e56

    </description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>

    <expand macro="requirements" />

    <expand macro="stdio" />

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

    <!-- Generate output files here because tin.py removes all instances of "bam"
    in the filename -->
    <command><![CDATA[
        #import re
        #set $input_list = []

        --sample-size=${samplesize} ${subtractbackground}
        && mv *summary.txt summary.tab
        && mv *tin.xls tin.xls
        ]]>
    </command>

    <inputs>
        <param name="input" type="data" format="bam" multiple="true" label="Input BAM file" help="(--input-file)"/>
        <expand macro="refgene_param" />
        <param name="minCov" type="integer" value="10" label="Minimum coverage (default=10)"
            help="Minimum number of reads mapped to a transcript (--minCov)." />
        <param name="samplesize" type="integer" value="100" label="Sample size (default=100)"
            help="Number of equal-spaced nucleotide positions picked from mRNA.
            Note: if this number is larger than the length of mRNA (L), it will
            be halved until is's smaller than L. (--sample-size)." />
        <param name="subtractbackground" type="boolean" value="false" falsevalue=""
            truevalue="--subtract-background" label="Subtract background noise
            (default=No)" help="Subtract background noise (estimated from
            intronic reads). Only use this option if there are substantial
            intronic reads (--subtract-background)." />
    </inputs>

    <outputs>
        <data name="outputsummary" format="tabular" from_work_dir="summary.tab" label="TIN on ${on_string} (summary)" />
        <data name="outputxls" format="tabular" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)" />
    </outputs>

    <!-- PDF Files contain R version, must avoid checking for diff -->
    <tests>
        <test expect_num_outputs="2">
            <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="outputsummary" file="summary.tin.txt" ftype="tabular"/>
            <output name="outputxls" file="output.tin.xls" ftype="tabular"/>
        </test>
    </tests>

    <help><![CDATA[
## tin.py

This program is designed to evaluate RNA integrity at transcript level. TIN
(transcript integrity number) is named in analogous to RIN (RNA integrity

@ABOUT@

]]>
    </help>

    <expand macro="citations" />

</tool>

63:27e16a30667a

    </description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <version_command><![CDATA[tin.py --version]]></version_command>
    <!-- Generate output files here because tin.py removes all instances of "bam"
    in the filename -->
    <command><![CDATA[
        #import re
        #set $input_list = []

        --sample-size=${samplesize} ${subtractbackground}
        && mv *summary.txt summary.tab
        && mv *tin.xls tin.xls
        ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="bam" multiple="true" label="Input BAM file" help="(--input-file)"/>
        <expand macro="refgene_param"/>
        <param name="minCov" type="integer" value="10" label="Minimum coverage (default=10)" help="Minimum number of reads mapped to a transcript (--minCov)."/>
        <param name="samplesize" type="integer" value="100" label="Sample size (default=100)" help="Number of equal-spaced nucleotide positions picked from mRNA.             Note: if this number is larger than the length of mRNA (L), it will             be halved until is's smaller than L. (--sample-size)."/>
        <param name="subtractbackground" type="boolean" value="false" falsevalue="" truevalue="--subtract-background" label="Subtract background noise             (default=No)" help="Subtract background noise (estimated from             intronic reads). Only use this option if there are substantial             intronic reads (--subtract-background)."/>
    </inputs>
    <outputs>
        <data name="outputsummary" format="tabular" from_work_dir="summary.tab" label="TIN on ${on_string} (summary)"/>
        <data name="outputxls" format="tabular" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)"/>
    </outputs>
    <!-- PDF Files contain R version, must avoid checking for diff -->
    <tests>
        <test expect_num_outputs="2">
            <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="outputsummary" file="summary.tin.txt" ftype="tabular"/>
            <output name="outputxls" file="output.tin.xls" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
## tin.py

This program is designed to evaluate RNA integrity at transcript level. TIN
(transcript integrity number) is named in analogous to RIN (RNA integrity

@ABOUT@

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