comparison chira_collapse.xml @ 15:00187b27f5e5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73"

14:2b2bfeda00d0

<tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@0">
    <description>deduplicate fastq reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />    
    <command><![CDATA[
        chira_collapse.py
        -i '$in'
        -u '$umi_len'
        -o '$out'
    ]]></command>

    <inputs>
        <param format="fastq" name="in" type="data" label="Input FASTQ file"/>
        <param name="umi_len" type="integer" value="0"
               label="Length of the UMI if present at the 5' end of your reads"/>
    </inputs>
    <outputs>
        <data format="fasta" name="out" label="ChiRA collapse FASTQ on ${on_string}"/>
    </outputs>

    <tests>
        <test expect_num_outputs="1">
            <param name="in" value="reads.fastq" />
            <output name="out" file="reads.fasta" />
        </test>
    </tests>

    <help>

15:00187b27f5e5

<tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@1">
    <description>deduplicate fastq reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />    
    <command><![CDATA[
        chira_collapse.py
        -i 
        #if $in.ext.endswith(".gz")
            <(gunzip -c '$in')
        #else
            '$in'
        #end if
        -u '$umi_len'
        -o '$out'
    ]]></command>

    <inputs>
        <param format="fastq,fastq.gz" name="in" type="data" label="Input FASTQ file"/>
        <param name="umi_len" type="integer" value="0"
               label="Length of the UMI if present at the 5' end of your reads"/>
    </inputs>
    <outputs>
        <data format="fasta" name="out" label="ChiRA collapse FASTQ on ${on_string}"/>
    </outputs>

    <tests>
        <test expect_num_outputs="1">
            <param name="in" value="reads.fastq.gz" ftype="fastq.gz"/>
            <output name="out" file="reads.fasta" />
        </test>
    </tests>

    <help>