comparison cutadapt.xml @ 22:093678460093 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"

21:104d86c98776

<tool id="cutadapt" name="Cutadapt" version="1.16.7" profile="17.09">
    <description>Remove adapter sequences from Fastq/Fasta</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>

    --minimum-length=$filter_options.min
#end if
#if str($filter_options.max):
    --maximum-length=$filter_options.max
#end if
#if $filter_options.max_n:
    --max-n=$filter_options.max_n
#end if
#if str( $library.type ) != "single":
    #if $filter_options.pair_filter:
        --pair-filter=$filter_options.pair_filter

#if str($read_mod_options.nextseq_trim) != '0':
    --nextseq-trim=$read_mod_options.nextseq_trim
#end if
$read_mod_options.trim_n
#if $read_mod_options.prefix != '':
    --prefix="$read_mod_options.prefix"
#end if
#if $read_mod_options.suffix != '':
    --suffix="$read_mod_options.suffix"
#end if
#if str($read_mod_options.length) != '0':
    --length=$read_mod_options.length
#end if
#if $read_mod_options.length_tag != '':
    --length-tag="$read_mod_options.length_tag"
#end if

'${read1}'
#if $paired:
    '${read2}'

            <param name="adapter2" value="AGATCGGAAGAGC"/>
            <section name="filter_options">
                <param name="discard_untrimmed" value="true"/>
                <param name="min" value="1"/>
                <param name="max" value="1000"/>
                <param name="max_n" value="1"/>
                <param name="pair_filter" value="both"/>
            </section>
            <assert_command>
                <has_text text="--discard-untrimmed"/>
                <has_text text="--minimum-length=1"/>
                <has_text text="--maximum-length=1000"/>
                <has_text text="--max-n=1"/>
                <has_text text="--pair-filter=both"/>
            </assert_command>
        </test>
    </tests>

22:093678460093

<tool id="cutadapt" name="Cutadapt" version="1.16.8" profile="17.09">
    <description>Remove adapter sequences from Fastq/Fasta</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>

    --minimum-length=$filter_options.min
#end if
#if str($filter_options.max):
    --maximum-length=$filter_options.max
#end if
#if str($filter_options.max_n):
    --max-n=$filter_options.max_n
#end if
#if str( $library.type ) != "single":
    #if $filter_options.pair_filter:
        --pair-filter=$filter_options.pair_filter

#if str($read_mod_options.nextseq_trim) != '0':
    --nextseq-trim=$read_mod_options.nextseq_trim
#end if
$read_mod_options.trim_n
#if $read_mod_options.prefix != '':
    --prefix='$read_mod_options.prefix'
#end if
#if $read_mod_options.suffix != '':
    --suffix='$read_mod_options.suffix'
#end if
#if str($read_mod_options.length) != '0':
    --length=$read_mod_options.length
#end if
#if $read_mod_options.length_tag != '':
    --length-tag='$read_mod_options.length_tag'
#end if

'${read1}'
#if $paired:
    '${read2}'

            <param name="adapter2" value="AGATCGGAAGAGC"/>
            <section name="filter_options">
                <param name="discard_untrimmed" value="true"/>
                <param name="min" value="1"/>
                <param name="max" value="1000"/>
                <param name="max_n" value="0"/>
                <param name="pair_filter" value="both"/>
            </section>
            <assert_command>
                <has_text text="--discard-untrimmed"/>
                <has_text text="--minimum-length=1"/>
                <has_text text="--maximum-length=1000"/>
                <has_text text="--max-n=0"/>
                <has_text text="--pair-filter=both"/>
            </assert_command>
        </test>
    </tests>