annotate bamsort.xml @ 1:bfcd121b99bf draft default tip

planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 44e872b808f88eacd05963fc2478da2c07b50228

<tool id="mimodd_sort" name="MiModD Sort" version="@MIMODD_WRAPPER_VERSION@">
    <description>takes a SAM/BAM dataset and generates a coordinate/name-sorted copy</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
	mimodd sort '$input.ifile' 
	    -o '$ofile' --iformat $input.iformat --oformat $oformat $by_name
    </command>
  
    <inputs>
        <conditional name="input">
            <param name="iformat" type="select" label="Input data format">
                <option value="bam">bam</option>
                <option value="sam">sam</option>
            </param>
            <when value="bam">
                <param name="ifile" type="data" format="bam" 
                label="BAM input dataset to sort" />
            </when>
            <when value="sam">
                <param name="ifile" type="data" format="sam" 
                label="SAM input dataset to sort" />
            </when>
        </conditional>
        <param name="oformat" type="select" label="Output format for the sorted data">
            <option value="bam">bam</option>
            <option value="sam">sam</option>
        </param>
        <param name="by_name" type="boolean" truevalue="-n" falsevalue="" checked="false"
        label="Sort by read names instead of coordinates"
        help="A less common option, but necessary, e.g., if you want to re-align coordinate sorted paired-end reads with the MiModD Read Alignment Tool or other NGS mapping tools." />
    </inputs>
  
    <outputs>
        <data name="ofile" format="bam" 
        label="Sorted output from MiModd ${tool.name} on ${on_string}">
            <change_format>
	            <when input="oformat" value="sam" format="sam" />
            </change_format>
        </data>
    </outputs>
    
    <tests>
        <test>
            <conditional name="input">
                <param name="iformat" value="sam" />
                <param name="ifile" value="header_only.sam" />
            </conditional>
            <param name="oformat" value="bam" />
            <assert_command>
                <not_has_text text="-n" />
            </assert_command>
            <output name="ofile" ftype="bam" file="so_coordinate.bam" />
        </test>
        <test>
            <conditional name="input">
                <param name="iformat" value="bam" />
                <param name="ifile" value="header_only.bam" />
            </conditional>
            <param name="oformat" value="sam" />
            <param name="by_name" value="true" />
            <assert_command>
                <has_text text=" -n" />
            </assert_command>
            <output name="ofile" ftype="sam" file="so_queryname.sam" />
        </test>
    </tests>

    <help><![CDATA[
.. class:: infomark

   **What it does**

The tool sorts an aligned reads input dataset, typically by the reference
genome coordinates that the reads have been mapped to.

Coordinate-sorted input files are expected by most downstream MiModD tools, but
note that the *MiModD Read Alignment* produces coordinate-sorted output by
default and it is only necessary to sort files that come from other sources or
from *MiModD Read Alignment* jobs with a custom sort order.

The option *Sort by read names instead of coordinates* is useful if you want to
re-align coordinate-sorted paired-end data. In *paired-end mode*, the
*MiModD Read Alignment* tool expects the reads in the input file to be arranged
in read pairs, *i.e.*, the forward read information of a pair must be followed
immediately by its reverse mate information, which is typically not the case in
coordinate-sorted data. Resorting such data by read names fixes this problem.

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