comparison bismark_bowtie2_wrapper.xml @ 38:b2d0e92f81c2 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"

37:79df147da633

                <!-- 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."/>
                <param argument="--pbat" name="pbat" type="boolean"
                       truevalue="--pbat" falsevalue="" checked="false"
                       label="Treat input data as PBAT-Seq libraries"
                       help="Use this option only if you are certain that your libraries were constructed following a PBAT protocol. If you don't know what PBAT-Seq is you should not specify this option." />

            <output name="output" file="mapped_reads_mate.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
        </test>
        <test>
            <param name="genomeSource" value="history"/>
            <param name="own_file" value="mm10.tiny.fa.gz" />
            <param name="sPaired" value="single"/>
            <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/>
            <param name="sort_bam" value="false"/>
            <param name="settingsType" value="custom"/>
            <param name="suppressed_read_file" value="true"/>

38:b2d0e92f81c2

                <!-- 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."/>
                <param argument="--pbat" name="pbat" type="boolean"
                       truevalue="--pbat" falsevalue="" checked="false"
                       label="Treat input data as PBAT-Seq libraries"
                       help="Use this option only if you are certain that your libraries were constructed following a PBAT protocol. If you don't know what PBAT-Seq is you should not specify this option." />

            <output name="output" file="mapped_reads_mate.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
        </test>
        <test>
            <param name="genomeSource" value="history"/>
            <param name="own_file" value="mm10.tiny.fa.gz" />
            <param name="sPaired" value="paired"/>
            <repeat name="mate_list">
                <param name="input_mate1" value="input1.fq" ftype="fastqsanger"/>
                <param name="input_mate2" value="input1.fq" ftype="fastqsanger"/>
            </repeat>
            <repeat name="mate_list">
                <param name="input_mate1" value="input2.fq" ftype="fastqsanger"/>
                <param name="input_mate2" value="input2.fq" ftype="fastqsanger"/>
            </repeat>
            <param name="sort_bam" value="false"/>
            <param name="settingsType" value="custom"/>
            <param name="suppressed_read_file" value="true"/>
            <param name="unmapped_read_file" value="true"/>
            <param name="bismark_stdout" value="true"/>
            <param name="isReportOutput" value="true"/>

            <output name="output_stdout" file="summary_mate_two_samples.txt" ftype="txt" lines_diff="94">
                 <assert_contents>
                     <has_text text="Sequence pairs analysed in total:" />
                     <has_text text="1000" />
                     <has_text text="Mapping efficiency:" />
                     <has_text text="0.0%" />
                     <has_text text="Bismark run complete" />
                 </assert_contents>
            </output>
            <output name="report_file" file="mapping_report_mate_two_samples.txt" ftype="txt" lines_diff="12"/>
            <output name="output" file="mapped_reads_mate_two_samples.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
        </test>
        <test>
            <param name="genomeSource" value="history"/>
            <param name="own_file" value="mm10.tiny.fa.gz" />
            <param name="sPaired" value="single"/>
            <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/>
            <param name="sort_bam" value="false"/>
            <param name="settingsType" value="custom"/>
            <param name="suppressed_read_file" value="true"/>