comparison mircounts.xml @ 4:da1aa7de2b19 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d

3:6b8adacd4750

<tool id="mircounts" name="miRcounts" version="0.9.3">
    <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">bowtie</requirement>
        <requirement type="package" version="1.4.1">samtools</requirement>
        <requirement type="package" version="0.11.2.1">pysam</requirement>
        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
        <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ## To be refactored with guidelines in https://github.com/ARTbio/tools-artbio/issues/140
        wget ftp://mirbase.org/pub/mirbase/CURRENT/genomes/${genomeKey}.gff3 && ## download gff3 specified by the variable genomeKey
        python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
        wget ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gz &&
        sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey &&
        #if $cutadapt.cutoption == "yes":

            <options from_data_table="miRbase_GenomeKeys">
                <column name="name" index="1"/>
                <column name="value" index="0"/>
            </options>
        </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">
            <option value="0">0</option>
            <option selected="true" value="1">1</option>
            <option value="2">2</option>
            <option value="3">3</option>

        </conditional>
    </inputs>
    <outputs>
        <data format="bam" label="BAM alignment" name="output" />
        <data format="gff3" label="GFF3 generated by miRCounts" name="gff3"/>
        <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file" />
        <data format="tabular" label="Mir Counts" name="mir_count_file" />
        <data format="tabular" label="Coverage Table" name="coverage_dataframe">
            <filter>plotting['plottingOption'] == "yes"</filter>
        </data>
        <data format="pdf" label="Pre-mir coverage (${plotting.display})" name="latticePDF">
            <filter>plotting['plottingOption'] == "yes"</filter>

4:da1aa7de2b19

<tool id="mircounts" name="miRcounts" version="0.9.4">
    <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">bowtie</requirement>
        <requirement type="package" version="1.4.1">samtools</requirement>
        <requirement type="package" version="0.11.2.1">pysam</requirement>
        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
        <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        wget ftp://mirbase.org/pub/mirbase/CURRENT/genomes/${genomeKey}.gff3 && ## download gff3 specified by the variable genomeKey
        python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
        wget ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gz &&
        sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey &&
        #if $cutadapt.cutoption == "yes":

            <options from_data_table="miRbase_GenomeKeys">
                <column name="name" index="1"/>
                <column name="value" index="0"/>
            </options>
        </param>
        <!-- work on proper selection of the url (that varies between gff, gff2 and gff3)
        <param name="mirbase_version" type="select" label="Choose miRbase version">
            <option selected="true" value="CURRENT">Current</option>
            <option value="1.0">1.0</option>
            <option value="1.1">1.1</option>
            <option value="1.2">1.2</option>
            <option value="1.3">1.3</option>
            <option value="1.4">1.4</option>
            <option value="1.5">1.5</option>
            <option value="2.0">2.0</option>
            <option value="2.1">2.0</option>
            <option value="2.2">2.2</option>
            <option value="3.0">3.0</option>
            <option value="3.1">3.1</option>
            <option value="4.0">4.0</option>
            <option value="5.0">5.0</option>
            <option value="5.1">5.1</option>
            <option value="6.0">6.0</option>
            <option value="7.0">7.0</option>
            <option value="7.1">7.1</option>
            <option value="8.0">8.0</option>
            <option value="8.1">8.1</option>
            <option value="8.2">8.2</option>
            <option value="9.0">9.0</option>
            <option value="9.1">9.1</option>
            <option value="9.2">9.2</option>
            <option value="10.0">10.0</option>
            <option value="10.1">10.1</option>
            <option value="11.0">11.0</option>
            <option value="12.0">12.0</option>
            <option value="13.0">13.0</option>
            <option value="14">14</option>
            <option value="15">15</option>
            <option value="16">16</option>
            <option value="17">17</option>
            <option value="18">18</option>
            <option value="19">19</option>
            <option value="20">20</option>
            <option value="21">21</option>
            </options>
        </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">
            <option value="0">0</option>
            <option selected="true" value="1">1</option>
            <option value="2">2</option>
            <option value="3">3</option>

        </conditional>
    </inputs>
    <outputs>
        <data format="bam" label="BAM alignment" name="output" />
        <data format="gff3" label="GFF3 generated by miRCounts" name="gff3"/>
        <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file">
            <actions>
                <action name="column_names" type="metadata" default="Gene,Counts" />
            </actions>
        </data>
        <data format="tabular" label="Mir Counts" name="mir_count_file">
            <actions>
                <action name="column_names" type="metadata" default="Gene,Counts" />
            </actions>
        </data>
        <data format="tabular" label="Coverage Table" name="coverage_dataframe">
            <filter>plotting['plottingOption'] == "yes"</filter>
        </data>
        <data format="pdf" label="Pre-mir coverage (${plotting.display})" name="latticePDF">
            <filter>plotting['plottingOption'] == "yes"</filter>