annotate cmpress.xml @ 5:6e18e0b098cd draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86

<tool id="infernal_cmpress" name="cmpress" version="@VERSION@.0">
    <description> Prepare a covariance model database for cmscan</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
    ## CM file from the history or stored as database on disc
    #if str($cm_opts.cm_opts_selector) == "db":
        cmfile_path='$cm_opts.database.fields.path'
    #else:
        ##'$cm_opts.cmfile'
        cmfile_path='$cmfile'
    #end if
    &&
    cmpress -F "\$cmfile_path" &&
    ##cmpress creates four files in the same directory of the cm file
    cd `dirname "\$cmfile_path"` &&
    tar -cvf '$outfile' `basename "\$cmfile_path"`.i1*
]]>
    </command>
    <inputs>
        <conditional name="cm_opts">
            <param name="cm_opts_selector" type="select" label="Subject covariance models &lt;cmdb&gt; ">
                <option value="db" >Locally installed covariance models</option>
                <option value="histdb" selected="True">Covariance model from your history</option>
            </param>
            <when value="db">
                <param name="database" type="select" label="Covariance models">
                    <options from_file="infernal.loc">
                        <column name="value" index="0"/>
                        <column name="name" index="1"/>
                        <column name="path" index="2"/>
                    </options>
                </param>
            </when>
            <when value="histdb">
                <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
            </when>
        </conditional>

    </inputs>
    <outputs>
        <data format="tar" name="outfile" label="cmpress on ${on_string}"/>
    </outputs>

    <tests>
        <test>
            <conditional name="cm_opts">
                <param name="cm_opts_selector" value="histdb"/>
                <param name="cmfile" value="cmpress_input_minifam.cm"/>
            </conditional>
            <assert_stdout>
                    <has_text text="Working...    done."/>
            </assert_stdout>

        </test>

    </tests>
    <help>
<![CDATA[


**What it does**

Starting from a CM database <cmfile> in standard Infernal-1.1 format, construct binary compressed datafiles for cm-
scan. The cmpress step is required for cmscan to work.

**Input format**

The <cmfile> must be have already been calibrated with cmcalibrate for cmpress to work.

**Output format**



For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_.


]]>
    </help>

    <expand macro="citations" />


</tool>