comparison mircounts.xml @ 13:b045c30fb768 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"

12:6d3e98cba73a

<tool id="mircounts" name="miRcounts" version="1.3.2">
    <description> Counts miRNA alignments from small RNA sequence data</description>
    <requirements>
        <requirement type="package" version="1.2.0">bowtie</requirement>
        <requirement type="package" version="1.6.0">samtools</requirement>
        <requirement type="package" version="0.11.2.2">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>
    <stdio>
        <exit_code range="1:" level="warning" description="Tool exception" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[

                                                --Nmode $cutadapt.Nmode &&
        #else:
            ln -f -s '$cutadapt.clipped_input' clipped_input.fastq &&
        #end if
        bowtie-build hairpin.fa hairpin &&
        bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -O bam -o '$output' &&
        samtools index $output &&
        python '$__tool_directory__'/mircounts.py --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe
        #if $plotting.plottingOption == 'yes':
            && Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF
        #end if

            <filter>plotting['plottingOption'] == "yes"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="cutoption" value="yes" />
            <param name="min" value="18"/>
            <param name="max" value="32"/>
            <param name="Nmode" value="reject"/>
            <param name="clip_sequence" value="TGGAATTCTCGGGTGCCAAG"/>

13:b045c30fb768

<tool id="mircounts" name="miRcounts" version="1.4.0">
    <description> Counts miRNA alignments from small RNA sequence data</description>
    <requirements>
        <requirement type="package" version="1.2.0">bowtie</requirement>
        <requirement type="package" version="1.9=h10a08f8_12">samtools</requirement>
        <requirement type="package" version="0.15.3=py27hda2845c_1">pysam</requirement>
        <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement>
        <requirement type="package" version="0.20_38=r36hcdcec82_1002">r-lattice</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="warning" description="Tool exception" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[

                                                --Nmode $cutadapt.Nmode &&
        #else:
            ln -f -s '$cutadapt.clipped_input' clipped_input.fastq &&
        #end if
        bowtie-build hairpin.fa hairpin &&
        bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '$output' &&
        samtools index $output &&
        python '$__tool_directory__'/mircounts.py --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe
        #if $plotting.plottingOption == 'yes':
            && Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF
        #end if

            <filter>plotting['plottingOption'] == "yes"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="cutoption" value="no" />
            <param name="v" value="1"/>
            <param name="genomeKey" value="aga"/>
            <param name="mirbase_version" value="22"/>
            <param name="clipped_input" value="aga.fastqsanger" ftype="fastqsanger"/>
            <param name="plottingOption" value="yes"/>
            <param name="display" value="relative"/>
            <param name="output_premir_counts" value="True"/>
            <param name="output_mir_counts" value="True"/>
            <output name="output" file="aga.bam"/>
            <output name="gff3" file="aga.22.gff3" lines_diff="22"/>
            <output name="pre_mir_count_file" file="aga_pre_mirs_count.22.tab"/>
            <output name="mir_count_file" file="aga_mirs_count.22.tab"/>
            <output name="latticePDF" file="aga_mir_coverage.pdf"/>
            <output name="coverage_dataframe" file="aga_lattice_dataframe.tab"/>
        </test>
        <test>
            <param name="cutoption" value="yes" />
            <param name="min" value="18"/>
            <param name="max" value="32"/>
            <param name="Nmode" value="reject"/>
            <param name="clip_sequence" value="TGGAATTCTCGGGTGCCAAG"/>