comparison bowtie2_wrapper.xml @ 20:dc1639b66f12 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 1912a560c3ad87117f18570fcf3ba4af4f924340

19:97d1923c8c4b

<tool id="bowtie2" name="Bowtie2" version="2.3.4" profile="17.01">
    <description>- map reads against reference genome</description>
    <macros>
        <import>bowtie2_macros.xml</import>
    </macros>
    <requirements>

    #end if

    #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
        ${analysis_type.sam_options.no_unal}
        ${analysis_type.sam_options.omit_sec_seq}
        ${analysis_type.sam_options.sam-no-qname-trunc}
        ${analysis_type.sam_options.xeq}
        ${analysis_type.sam_options.soft-clipped-unmapped-tlen}
    #end if

    #if str( $analysis_type.other_options.other_options_selector ) == "yes":
        ${analysis_type.other_options.reorder}
        ${analysis_type.other_options.non_deterministic}

                        <option value="no" selected="true">No</option>
                    </param>
                    <when value="yes">
                        <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
                        <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
                        <param argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
                        <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
                        <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
                    </when>
                    <when value="no">
                        <!-- do nothing -->
                    </when>
                </conditional>

20:dc1639b66f12

<tool id="bowtie2" name="Bowtie2" version="2.3.4.1" profile="17.01">
    <description>- map reads against reference genome</description>
    <macros>
        <import>bowtie2_macros.xml</import>
    </macros>
    <requirements>

    #end if

    #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
        ${analysis_type.sam_options.no_unal}
        ${analysis_type.sam_options.omit_sec_seq}
        ${analysis_type.sam_options.sam_no_qname_trunc}
        ${analysis_type.sam_options.xeq}
        ${analysis_type.sam_options.soft_clipped_unmapped_tlen}
    #end if

    #if str( $analysis_type.other_options.other_options_selector ) == "yes":
        ${analysis_type.other_options.reorder}
        ${analysis_type.other_options.non_deterministic}

                        <option value="no" selected="true">No</option>
                    </param>
                    <when value="yes">
                        <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
                        <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
                        <param name="sam_no_qname_trunc" argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
                        <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
                        <param name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
                    </when>
                    <when value="no">
                        <!-- do nothing -->
                    </when>
                </conditional>