comparison umi-tools_extract.xml @ 1:79436b3019e9 draft

planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36

0:418b961e0576

<tool id="umi_tools_extract" name="UMI-tools extract" version="0.4.4.0">
    <description>Extract UMI from fastq files</description>
    <requirements>
        <requirement type="package" version="0.4.4">umi_tools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #set $gz = False
        #if $input_type.type == 'single':
            #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
                ln -s '$input_type.input_single' input_single.gz &&

            <param name="prime3" value="0" />
            <param name="quality_selector" value="true" />
            <param name="quality_filter_threshold" value="10" />
            <param name="quality_encoding" value="phred33" />
            <output name="out" file="out_SE.fastq" />
            <output name="out_log" file="out_single.log" lines_diff="15"/>
        </test>
        <test>
            <param name="type" value="paired" />
            <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" />
            <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" />
            <param name="bc_pattern" value="NNNXXX" />
            <output name="out1" file="out_R1.fastq.gz" decompress="true" />
            <output name="out2" file="out_R2.fastq.gz" decompress="true" />
            <output name="out_log" file="out_paired.log" lines_diff="10"/>
        </test>
    </tests>
    <help><![CDATA[

reads end one from stdin and end two from FASTQIN and outputs end one to stdin
and end two to FASTQOUT.

    ]]></help>
    <citations>
        <citation type="doi">10.1101/gr.209601.116</citation>
        <citation type="bibtex">
            @misc{githubUMI-tools,
            title = {UMI-tools},
            publisher = {GitHub},
            journal = {GitHub repository},
            url = {https://github.com/CGATOxford/UMI-tools},
            }
        </citation>
    </citations>
</tool>

1:79436b3019e9

<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.0">
    <description>Extract UMI from fastq files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #set $gz = False
        #if $input_type.type == 'single':
            #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
                ln -s '$input_type.input_single' input_single.gz &&

            <param name="prime3" value="0" />
            <param name="quality_selector" value="true" />
            <param name="quality_filter_threshold" value="10" />
            <param name="quality_encoding" value="phred33" />
            <output name="out" file="out_SE.fastq" />
            <output name="out_log" file="out_single.log" lines_diff="22"/>
        </test>
        <test>
            <param name="type" value="paired" />
            <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" />
            <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" />
            <param name="bc_pattern" value="NNNXXX" />
            <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" />
            <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" />
            <output name="out_log" file="out_paired.log" lines_diff="16"/>
        </test>
    </tests>
    <help><![CDATA[

reads end one from stdin and end two from FASTQIN and outputs end one to stdin
and end two to FASTQOUT.

    ]]></help>
    <expand macro="citations" />
</tool>