comparison damidseq_core.xml @ 4:b07936a3962d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1

3:e47f77820200

    <requirements>
        <requirement type="package" version="1.4">damidseq_pipeline</requirement>
    </requirements>
    <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
    <command detect_errors="aggressive"><![CDATA[
        ln -f -s '$dam' A001.fastq &&
        ln -f -s '$dam_fusion' A002.fastq &&
        ln -f -s '$index' index.txt &&
        HOME="\$PWD" damidseq_pipeline
        --bins=$bins
        --bowtie=1
        --bowtie2_genome_dir='$reference_index.fields.path'

        <configfile name="index">A1	Dam
A2	Fusion</configfile>
    </configfiles>
    <inputs>
        <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
        <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
        <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
          <options from_data_table="bowtie2_indexes">
            <filter type="sort_by" column="2"/>
            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
          </options>

            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="dam" value="A001.fastq"/>
            <param name="dam_fusion" value="A002.fastq"/>
            <param name="gatc_frag_file" value="dm6.GATC.gff"/>
            <param name="reference_index" value="dm6"/>
            <param name="norm_method" value="rpm"/>
            <output name="output_ratio" file="output_ratio.bed"/>
            <output name="control_output" file="control.bam"/>

4:b07936a3962d

    <requirements>
        <requirement type="package" version="1.4">damidseq_pipeline</requirement>
    </requirements>
    <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
    <command detect_errors="aggressive"><![CDATA[
        ln -f -s '$dam_fusion' A002.fastq &&
        ln -f -s '$dam_only' A001.fastq &&
        ln -f -s '$index' index.txt &&
        HOME="\$PWD" damidseq_pipeline
        --bins=$bins
        --bowtie=1
        --bowtie2_genome_dir='$reference_index.fields.path'

        <configfile name="index">A1	Dam
A2	Fusion</configfile>
    </configfiles>
    <inputs>
        <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
        <param name="dam_only" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
        <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
          <options from_data_table="bowtie2_indexes">
            <filter type="sort_by" column="2"/>
            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
          </options>

            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="dam_fusion" value="A002.fastq"/>
            <param name="dam_only" value="A001.fastq"/>
            <param name="gatc_frag_file" value="dm6.GATC.gff"/>
            <param name="reference_index" value="dm6"/>
            <param name="norm_method" value="rpm"/>
            <output name="output_ratio" file="output_ratio.bed"/>
            <output name="control_output" file="control.bam"/>