view cmpress.xml @ 10:3711f654044e draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 4fecc1be8a950820a469f6bb5e252ae7dfc59b7b

<tool id="infernal_cmpress" name="cmpress" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <description> Prepare a covariance model database for cmscan</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command detect_errors="aggressive">
<![CDATA[
    mkdir -p ./cm_model &&
    #if str($cm_opts.cm_opts_selector) == "db":
        ln -s '$cm_opts.database.fields.path' ./cm_model/
    #else:
        ln -s '$cmfile' ./cm_model/
    #end if
    &&
    cmpress -F ./cm_model/* &&
    cd ./cm_model/ &&
    tar -cvf '$outfile' *.i1f *.i1i *.i1m *.i1p
]]>
    </command>
    <inputs>
        <expand macro="DB" />
    </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>
        <test>
            <conditional name="cm_opts">
                <param name="cm_opts_selector" value="db"/>
                <param name="database" 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>