comparison trim_galore.xml @ 7:8352713cf939 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 07148c518916e16602ea26473d00358fe04bc3b6-dirty

6:11962ce40855

<tool id="trim_galore" name="Trim Galore!" version="0.4.0">
    <!-- Wrapper compatible with Trim Galore! version 0.4 -->
    <description>adaptive quality and adapter trimmer</description>
    <macros>
        <macro name="adapter_trimming">
            <conditional name="trimming">

                    <option value="--illumina">Illumina universal</option>
                    <option value="--nextera">Nextera transposase</option>
                    <option value="--small_rna">Illumina small RNA adapters</option>
                    <option value="user">User defined adapter trimming</option>
                </param>
                <when value="auto"/>
                <when value="--illumina"/>
                <when value="--nextera"/>
                <when value="--small_rna"/>
                <when value="user">
                    <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">

        <data format="fastqsanger" name="trimmed_reads_pair2" from_work_dir="input_mate2_val_2.fq"
            label="${tool.name} on ${on_string}: trimmed reads pair 2">
            <filter>singlePaired['sPaired'] == "paired"</filter>
        </data>

        <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_val_1.fq"
            label="${tool.name} on ${on_string}: unpaired reads (1)">
            <filter>params['settingsType'] == "custom"</filter>
            <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
            <filter>singlePaired['sPaired'] == "paired"</filter>
        </data>

        <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_val_2.fq"
            label="${tool.name} on ${on_string}: unpaired reads (2)">
            <filter>params['settingsType'] == "custom"</filter>
            <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
            <filter>singlePaired['sPaired'] == "paired"</filter>
        </data>

7:8352713cf939

<tool id="trim_galore" name="Trim Galore!" version="0.4.1">
    <!-- Wrapper compatible with Trim Galore! version 0.4 -->
    <description>adaptive quality and adapter trimmer</description>
    <macros>
        <macro name="adapter_trimming">
            <conditional name="trimming">

                    <option value="--illumina">Illumina universal</option>
                    <option value="--nextera">Nextera transposase</option>
                    <option value="--small_rna">Illumina small RNA adapters</option>
                    <option value="user">User defined adapter trimming</option>
                </param>
                <when value=""/>
                <when value="--illumina"/>
                <when value="--nextera"/>
                <when value="--small_rna"/>
                <when value="user">
                    <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">

        <data format="fastqsanger" name="trimmed_reads_pair2" from_work_dir="input_mate2_val_2.fq"
            label="${tool.name} on ${on_string}: trimmed reads pair 2">
            <filter>singlePaired['sPaired'] == "paired"</filter>
        </data>

        <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_unpaired_1.fq"
            label="${tool.name} on ${on_string}: unpaired reads (1)">
            <filter>params['settingsType'] == "custom"</filter>
            <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
            <filter>singlePaired['sPaired'] == "paired"</filter>
        </data>

        <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_unpaired_2.fq"
            label="${tool.name} on ${on_string}: unpaired reads (2)">
            <filter>params['settingsType'] == "custom"</filter>
            <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
            <filter>singlePaired['sPaired'] == "paired"</filter>
        </data>