comparison fastp.xml @ 12:d60c3f704da0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f

11:c59d48774d03

<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy0" profile="23.1">
    <description>fast all-in-one preprocessing for FASTQ files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools" />

#end if

#if str($single_paired.single_paired_selector).startswith('paired'):
    #if str($single_paired.adapter_trimming_options.adapter_sequence2):
        --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
    #else
        --detect_adapter_for_pe
    #end if
#end if


## Global Trimming Options

            <when value="paired">
                <expand macro="in" read_number="1" argument="-i"/>
                <expand macro="in" read_number="2" argument="-I"/>
                <expand macro="adapter_trimming_options">
                    <expand macro="adapter_sequence" read_number="2"/>
                </expand>
                <expand macro="global_trimming_options_paired" />
            </when>
            <when value="paired_collection">
                <param name="paired_input" type="data_collection" format="fastq,fastq.gz" label="Select paired collection(s)" collection_type="paired"/>
                <expand macro="adapter_trimming_options">
                    <expand macro="adapter_sequence" read_number="2"/>
                </expand>
                <expand macro="global_trimming_options_paired" />
            </when>
        </conditional>

12:d60c3f704da0

<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy1" profile="23.1">
    <description>fast all-in-one preprocessing for FASTQ files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools" />

#end if

#if str($single_paired.single_paired_selector).startswith('paired'):
    #if str($single_paired.adapter_trimming_options.adapter_sequence2):
        --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
    #end if
    $single_paired.adapter_trimming_options.detect_adapter_for_pe
#end if


## Global Trimming Options

            <when value="paired">
                <expand macro="in" read_number="1" argument="-i"/>
                <expand macro="in" read_number="2" argument="-I"/>
                <expand macro="adapter_trimming_options">
                    <expand macro="adapter_sequence" read_number="2"/>
                    <expand macro="detect_adapter_for_pe" />
                </expand>
                <expand macro="global_trimming_options_paired" />
            </when>
            <when value="paired_collection">
                <param name="paired_input" type="data_collection" format="fastq,fastq.gz" label="Select paired collection(s)" collection_type="paired"/>
                <expand macro="adapter_trimming_options">
                    <expand macro="adapter_sequence" read_number="2"/>
                    <expand macro="detect_adapter_for_pe" />
                </expand>
                <expand macro="global_trimming_options_paired" />
            </when>
        </conditional>