annotate samtools_fastx.xml @ 0:a0d039fa9771 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4

<?xml version="1.0"?>
<tool id="samtools_fastx" name="Samtools extract" version="@TOOL_VERSION@">
    <description>FASTA or FASTQ from a SAM file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code">
    <![CDATA[
        samtools $output.output_format
            #if $output.output_format == 'fastq':
                -v $output.default_quality $output.output_quality
            #end if
            #if $reference:
                --reference '$reference'
            #end if
            $copy_flags $omit_read_number
            -0 '$nonspecific'
            -1 '$forward'
            -2 '$reverse'
            #if str($inclusive_filter) != 'None':
                #set $filter = $inclusive_filter
                @FLAGS@
                -f $flags
            #end if
            #if str($exclusive_filter) != 'None':
                #set $filter = $exclusive_filter
                @FLAGS@
                -F $flags
            #end if
            '$input'
    ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="bam,sam" label="BAM or SAM file to convert" />
        <param argument="--reference" type="data" format="fasta" optional="True" label="Reference FASTA" />
        <param name="copy_flags" argument="-t" type="boolean" truevalue="-t" falsevalue="" label="Copy RG/BC/QT flags to output header" />
        <param name="omit_read_number" argument="-n" type="boolean" truevalue="-n" falsevalue="" label="Do not append /1 and /2 to read names" />
        <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags be set">
            <expand macro="filter_options" />
        </param>
        <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with the following flags set">
            <expand macro="filter_options" />
        </param>
        <conditional name="output">
            <param name="output_format" type="select" label="Output format">
                <option value="fasta">FASTA</option>
                <option value="fastq">FASTQ</option>
            </param>
            <when value="fastq">
                <param name="default_quality" argument="-v" type="integer" value="1" label="Default quality if none is given" />
                <param name="output_quality" argument="-O" type="boolean" truevalue="-O" falsevalue="" label="Output quality in the OQ tag if available" />
            </when>
            <when value="fasta" />
        </conditional>
    </inputs>
    <outputs>
        <data name="nonspecific" format="fasta" label="${on_string} converted to ${output.output_format} (Neither or both)">
            <change_format>
                <when input="output_format" value="fastq" format="fastq" />
            </change_format>
        </data>
        <data name="forward" format="fasta" label="${on_string} converted to ${output.output_format} (READ1)">
            <change_format>
                <when input="output_format" value="fastq" format="fastq" />
            </change_format>
        </data>
        <data name="reverse" format="fasta" label="${on_string} converted to ${output.output_format} (READ2)">
            <change_format>
                <when input="output_format" value="fastq" format="fastq" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
            <param name="output_format" value="fasta" />
            <output name="nonspecific" file="samtools_fastx-out1-1.fasta" />
            <output name="forward" file="samtools_fastx-out1-2.fasta" />
            <output name="reverse" file="samtools_fastx-out1-3.fasta" />
        </test>
        <test>
            <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
            <param name="output_format" value="fastq" />
            <output name="nonspecific" file="samtools_fastx-out2-1.fastq" />
            <output name="forward" file="samtools_fastx-out2-2.fastq" />
            <output name="reverse" file="samtools_fastx-out2-3.fastq" />
        </test>
        <test>
            <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
            <param name="output_format" value="fasta" />
            <output name="nonspecific" file="samtools_fastx-out3-1.fasta" />
            <output name="forward" file="samtools_fastx-out3-2.fasta" />
            <output name="reverse" file="samtools_fastx-out3-3.fasta" />
        </test>
    </tests>
    <help>
        <![CDATA[
        This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a SAM or BAM file in FASTA or FASTQ format.
        ]]>
    </help>
    <expand macro="citations" />
</tool>