annotate cfsan_snp_pipeline_map_reads.xml @ 1:85e400e1f2dd draft default tip

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<tool id="cfsan_snp_pipeline_map_reads" name="CFSAN SNP Pipeline: map reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#set compressed =" False"
#if str($input_type_cond.input_type) == 'paired':
    #set forward = $input_type_cond.reads_collection.forward
    #set reverse = $input_type_cond.reads_collection.reverse
#end if
#if $forward.is_of_type("fastq.gz","fastqsanger.gz"):
    ln -s '$forward' forward.gz &&
    #set forward = 'forward.gz'
    #set compressed = "GZ"
#else if $forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
    ln -s '$forward' forward.bz2 &&
    #set forward = 'forward.bz2'
    #set compressed = "BZ2"
#end if
#if $reverse.is_of_type("fastq.gz","fastqsanger.gz"):
    ln -s '$reverse' reverse.gz &&
    #set reverse = 'reverse.gz'
    #set compressed = "GZ"
#else if $reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
    ln -s '$reverse' reverse.bz2 &&
    #set reverse = 'reverse.bz2'
    #set compressed = "BZ2"
#end if
bowtie2-build '$reference' --threads \${GALAXY_SLOTS:-4} 'reference' &&
bowtie2 -q -x reference -1 '$forward' -2 '$reverse' -p \${GALAXY_SLOTS:-4} --reorder -X 1000 -S '$output'
    ]]></command>
    <inputs>
        <conditional name="input_type_cond">
            <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
                <option value="paired" selected="true">List of dataset pairs</option>
                <option value="pair">Dataset pair</option>
            </param>
            <when value="pair">
                <param name="forward" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
                <param name="reverse" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
            </when>
            <when value="paired">
                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
            </when>
        </conditional>
        <expand macro="reference_cond"/>
    </inputs>
    <outputs>
        <data name="output" format="sam"/>
    </outputs>
    <tests>
        <test>
            <param name="reference" value="lambda_virus.fasta" ftype="fasta"/>
            <param name="input_type" value="pair"/>
            <param name="forward" value="sample1_1.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="reverse" value="sample1_2.fastq.gz" ftype="fastqsanger.gz"/>
            <output name="output" ftype="sam">
                <assert_contents>
                    <has_size value="7285613" delta="1000"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="reference" value="lambda_virus.fasta" ftype="fasta"/>
            <param name="input_type" value="paired"/>
            <param name="reads_collection">
                <collection type="paired">
                    <element name="forward" value="sample1_1.fastq.gz"/>
                    <element name="reverse" value="sample1_2.fastq.gz"/>
                </collection>
            </param>
            <output name="output" ftype="sam">
                <assert_contents>
                    <has_size value="7285613" delta="1000"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Aligns the sequence reads for a specified sample to a specified reference genome. The reads are
sorted, duplicates marked, and realigned around indels.

**More information**

CFSAN SNP Pipeline `call consensus documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#call-consensus>`_
    ]]></help>
    <expand macro="citations"/>
</tool>