comparison bismark_bowtie2_wrapper.xml @ 10:7bffcb6fc81d draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 23685f742f0b5cd5de871c285d247d560485b11b

9:1a88b0f2669f

<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0.1" profile="18.01">
    <description>Bisulfite reads mapper</description>
    <requirements>
        <requirement type="package" version="0.20.0">bismark</requirement>
        <requirement type="package" version="1.8">samtools</requirement>
        <requirement type="package" version="2.3.4.2">bowtie2</requirement>

                <!-- output Options -->
                <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false"
                       label="Write the bismark output and summary information to an extra file"/>
                <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true"
                       label="Offer all report files concatenated in one file (Mapping Report)"/>
                <param argument="--non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="false"
                       label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/>

                <!--end output options -->
            </when>  <!-- full -->
        </conditional>  <!-- params -->

10:7bffcb6fc81d

<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0.2" profile="18.01">
    <description>Bisulfite reads mapper</description>
    <requirements>
        <requirement type="package" version="0.20.0">bismark</requirement>
        <requirement type="package" version="1.8">samtools</requirement>
        <requirement type="package" version="2.3.4.2">bowtie2</requirement>

                <!-- output Options -->
                <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false"
                       label="Write the bismark output and summary information to an extra file"/>
                <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true"
                       label="Offer all report files concatenated in one file (Mapping Report)"/>
                <param argument="--non-directional" name="non_directional" type="boolean"
                       truevalue="--non-directional" falsevalue="" checked="false" 
                       label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/>

                <!--end output options -->
            </when>  <!-- full -->
        </conditional>  <!-- params -->