comparison bwameth.xml @ 6:b4e6819b25ef draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 6d44811a45b4f6fded1ec72450ed300318095ce4"

5:29bdbc353f20

<tool id="bwameth" name="bwameth" version="@TOOL_VERSION@" profile="17.01">
    <description>Fast and accurate aligner of BS-Seq reads.</description>
    <macros>
        <token name="@TOOL_VERSION@">0.2.2</token>
    </macros>
    <requirements>

#if $single_or_paired.single_or_paired_opts == 'single':
    $read1
#else:
    $read1 $read2
#end if
| samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam -
    ]]></command>
    <inputs>
        <conditional name="referenceSource">
            <param name="source" type="select" label="Select a genome reference from your history or a built-in index?">
                <option value="history" selected="True">Use one from the history</option>

            <param name="referenceSource" value="history" />
            <param name="reference" value="ref.fa.gz" />
            <param name="single_or_paired_opts" value="paired" />
            <param name="input_mate1" value="t_R1.fastq.gz"/>
            <param name="input_mate2" value="t_R2.fastq.gz"/>
            <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
        </test>
        <test>
            <param name="referenceSource" value="history" />
            <param name="reference" value="ref.fa.gz" />
            <param name="single_or_paired_opts" value="paired_collection" />

                <collection type="paired">
                    <element name="forward" value="t_R1.fastq.gz"/>
                    <element name="reverse" value="t_R2.fastq.gz"/>
                </collection>
            </param>
            <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

6:b4e6819b25ef

<tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy1" profile="20.05">
    <description>Fast and accurate aligner of BS-Seq reads.</description>
    <macros>
        <token name="@TOOL_VERSION@">0.2.2</token>
    </macros>
    <requirements>

#if $single_or_paired.single_or_paired_opts == 'single':
    $read1
#else:
    $read1 $read2
#end if
| samtools view --no-PG -u - | samtools sort --no-PG -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam -
    ]]></command>
    <inputs>
        <conditional name="referenceSource">
            <param name="source" type="select" label="Select a genome reference from your history or a built-in index?">
                <option value="history" selected="True">Use one from the history</option>

            <param name="referenceSource" value="history" />
            <param name="reference" value="ref.fa.gz" />
            <param name="single_or_paired_opts" value="paired" />
            <param name="input_mate1" value="t_R1.fastq.gz"/>
            <param name="input_mate2" value="t_R2.fastq.gz"/>
            <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff-->
        </test>
        <test>
            <param name="referenceSource" value="history" />
            <param name="reference" value="ref.fa.gz" />
            <param name="single_or_paired_opts" value="paired_collection" />

                <collection type="paired">
                    <element name="forward" value="t_R1.fastq.gz"/>
                    <element name="reverse" value="t_R2.fastq.gz"/>
                </collection>
            </param>
            <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff-->
        </test>
    </tests>
    <help><![CDATA[

**What it does**