comparison mircounts.xml @ 9:2a08a6eb471c draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102

8:3f62272192f9

<tool id="mircounts" name="miRcounts" version="1.2.0">
    <description> Counts miRNA alignments from small RNA sequence data</description>
    <requirements>
        <requirement type="package" version="1.18">gnu-wget</requirement>
        <requirement type="package" version="1.2.0">bowtie</requirement>
        <requirement type="package" version="1.6.0">samtools</requirement>

                <column name="name" index="1"/>
                <column name="value" index="0"/>
            </options>
        </param>
        <param name="mirbase_version" type="select" label="Choose miRbase version">
<!--            <option selected="true" value="22">22</option> # activate when gff parsing is fixed -->
            <option value="21">21</option>
            <option value="20">20</option>
            <option value="19">19</option>
        </param>
        <param help="command [ bowtie -v 0,1,2,3 -M 1 --best --strata --norc ] will be used. Specify a value for -v (number of mismatches allowed)" label="Number of mismatches allowed" name="v" type="select">

        <data format="pdf" label="Pre-mir coverage (${plotting.display})" name="latticePDF">
            <filter>plotting['plottingOption'] == "yes"</filter>
        </data>
    </outputs>
    <tests>
         <test>
            <param name="cutoption" value="yes" />
            <param name="min" value="15"/>
            <param name="max" value="25"/>
            <param name="Nmode" value="reject"/>

            <output name="output" file="unclipped.out.bam" ftype="bam"/>
            <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/>
            <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
            <output name="mir_count_file" file="mirs_unclipped_count.tab"/>
        </test>
       <test>
            <param name="cutoption" value="yes" />
            <param name="min" value="15"/>
            <param name="max" value="25"/>
            <param name="Nmode" value="reject"/>
            <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>

9:2a08a6eb471c

<tool id="mircounts" name="miRcounts" version="1.2.6">
    <description> Counts miRNA alignments from small RNA sequence data</description>
    <requirements>
        <requirement type="package" version="1.18">gnu-wget</requirement>
        <requirement type="package" version="1.2.0">bowtie</requirement>
        <requirement type="package" version="1.6.0">samtools</requirement>

                <column name="name" index="1"/>
                <column name="value" index="0"/>
            </options>
        </param>
        <param name="mirbase_version" type="select" label="Choose miRbase version">
            <option selected="true" value="22">22</option>
            <option value="21">21</option>
            <option value="20">20</option>
            <option value="19">19</option>
        </param>
        <param help="command [ bowtie -v 0,1,2,3 -M 1 --best --strata --norc ] will be used. Specify a value for -v (number of mismatches allowed)" label="Number of mismatches allowed" name="v" type="select">

        <data format="pdf" label="Pre-mir coverage (${plotting.display})" name="latticePDF">
            <filter>plotting['plottingOption'] == "yes"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="cutoption" value="yes" />
            <param name="min" value="15"/>
            <param name="max" value="25"/>
            <param name="Nmode" value="reject"/>
            <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
            <param name="v" value="0"/>
            <param name="genomeKey" value="dme"/>
            <param name="mirbase_version" value="22"/>
            <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/>
            <param name="plottingOption" value="no"/>
            <param name="output_premir_counts" value="True"/>
            <param name="output_mir_counts" value="True"/>
            <output name="output" file="unclipped.out.22.bam" ftype="bam"/>
            <output name="gff3" file="translated_dme.22.gff3" ftype="gff3" lines_diff="22"/>
            <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.22.tab"/>
            <output name="mir_count_file" file="mirs_unclipped_count.22.tab"/>
        </test>
         <test>
            <param name="cutoption" value="yes" />
            <param name="min" value="15"/>
            <param name="max" value="25"/>
            <param name="Nmode" value="reject"/>

            <output name="output" file="unclipped.out.bam" ftype="bam"/>
            <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/>
            <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
            <output name="mir_count_file" file="mirs_unclipped_count.tab"/>
        </test>
        <test>
            <param name="cutoption" value="yes" />
            <param name="min" value="15"/>
            <param name="max" value="25"/>
            <param name="Nmode" value="reject"/>
            <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>