view distmat.xml @ 0:af7528402a97 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer commit 00e6389df9248031e385772e94a02f00719f5cba

<tool id="revoluzer_distmat" name="Compute distance matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description>for gene orders</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <version_command>distmat --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        distmat
            -f '$f'
            $structure
            $sign
            $distance
            $duplicates
            $output_cond.output_sel
            #if $output_cond.output_sel == ""
                $output_cond.header
            #end if
            > '$out'
    ]]></command>
    <inputs>
        <param argument="-f" type="data" format="fasta" label="Gene orders"/>
        <param name="structure" type="select" label="Genome structure">
            <option value="">Circular</option>
            <option value="--lindir">Linear directed genomes (--lindir)</option>
            <option value="--linund">Linear undirected genomes (--linund)</option>
        </param>
        <param argument="--sign" type="boolean" truevalue="--sign" falsevalue="" label="Genomes are circular"/>
        <param name="distance" type="select" label="Distance" help="Note that the default on the old web site was to compute Breakpoint distances">
            <option value="--crex">CREx</option>
            <option value="">Inversion</option>
            <option value="-b">Breakpoint</option>
            <option value="-i -m">Common Intervals</option>
            <option value="-i -m --lw">Length weigthed common intervals</option>
        </param>
        <param name="duplicates" type="select" label="Remove duplicate gene orders">
            <option value="">No</option>
            <option value="-d">Yes</option>
            <option value="-D">Yes and print names of removed gene orders</option>
        </param>
        <conditional name="output_cond">
            <param name="output_sel" type="select" label="Output type">
                <option value="">Table</option>
                <option value="--nexus">Nexus</option>
                <option value="--list">List</option>
            </param>
            <when value="">
                <param argument="--header" type="boolean" truevalue="--header" falsevalue="" label="Include header in table"/>
            </when>
            <when value="--nexus"/>
            <when value="--list"/>
        </conditional>
    </inputs>
    <outputs>
        <data name="out" format="tabular"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="f" value="test.fas"/>
            <output name="out">
                <assert_contents>
                    <has_n_lines n="5"/>
                    <has_n_columns n="1"/> <!-- wo header 1st line is just the number of genomes -->
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="f" value="test.fas"/>
            <param name="distance" value="Breakpoint"/>
            <conditional name="output_cond">
                <param name="header" value="true"/>
            </conditional>
            <output name="out">
                <assert_contents>
                    <has_n_lines n="5"/>
                    <has_n_columns n="5"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

Usage
.....

Compute a distance matrix for gene orders of unichromosomal genomes with equal duplication free gene content,
e.g. mitochondrial gene orders. Several distance measures are available.

- CREx distance (Bernt et al 2007) all other distance measures have been implemented
  in this software package. 
- Inversion distance (Bergeron, Heber & Jens Stoye 2002)
- Number of Breakpoints (e.g. Sankoff, Blanchette 1997)
- Common Intervals (Bergeron, A., Chauve, C., de Montgolfier, F., and Raffinot, M., 2008) 
- Conserved Intervals (Bergeron, A., Blanchette, M., Chateau, A., and Chauve, C., 2004)

For the latter a distance is computed by subtracting the number from the maximum possible for the number of genes.

**Input**

@INPUT_FORMAT@

**Output**

A tabular file showing the distance matrix.

    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btm468</citation>
        <citation type="doi">10.1089/cmb.1998.5.555 </citation><!--Sankoff Blanchette-->
        <citation type="doi">10.1093/bioinformatics/18.suppl_2.s54</citation>
        <citation type="doi">10.1137/060651331</citation>
        <citation type="doi">10.1007/978-3-540-30219-3_2</citation>
    </citations>
</tool>