comparison blockbuster.xml @ 3:7c7ff7a3503f draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit e11f6de08dca72259d2286c442c5464b1f2236d6

2:0f3d3f9f120f

<tool id="blockbuster" name="blockbuster" version="0.1.1.1">
    <description>detects blocks of overlapping reads using a gaussian-distribution approach</description>
    <requirements>
        <requirement type="package" version="0.0.1.1">blockbuster</requirement>
    </requirements>
    <command>

            -minClusterHeight $minClusterHeight
            -minBlockHeight $minBlockHeight
            -scale $scale
            -merge $merge
            -tagFilter $tagFilter
            -print $print
            $input
            > data.blockbuster;
            #if str($print)=="1"
                awk '{if ($1 ~ /^>/) print $2"\t"$3"\t"$4"\t"$1"\t"$6"\t"$5"\t"$3"\t"$4; else print $2"\t"$3"\t"$4"\tblock_"$1"\t"$6"\t"$5"\t"$3"\t"$4}' data.blockbuster
            #else if str($print)=="2"
                awk '{if ($1 ~ /^>/) print $2"\t"$3"\t"$4"\t"$1"\t"$6"\t"$5"\t"$3"\t"$4; else print $1"\t"$2"\t"$3"\t"$3"\t"$4"\t"$5"\t"$6"\t"$2"\t"$3}' data.blockbuster
            #end if
            > $output
]]>
    </command>
    <inputs>
        <param name="input" type="data" format="bed" label="BED file containing read expressions"/>
        <param name="distance" type="integer" value="40" label="minimum distance between two clusters"/>

        <param name="minBlockHeight" type="float" value="1" label="minimum height (readno) of a block"/>
        <param name="scale" type="float" value="0.5" label="scale stddev for a single read"/>
        <param name="merge" type="integer" value="0" label="merge reads with almost similar means"/>
        <param name="tagFilter" type="integer" value="0" label="skip tags with expression smaller than this value"/>
        <param name="print" type="select" label="Type of output" >
            <option value="1">blocks</option>
            <option value="2" selected="True">reads</option>
        </param>
    </inputs>

    <outputs>
        <data format="bed" name="output" label="blockbuster on ${on_string}"/>
    </outputs>
    <help>
<![CDATA[

**What it does**

3:7c7ff7a3503f

<tool id="blockbuster" name="blockbuster" version="0.1.2">
    <description>detects blocks of overlapping reads using a gaussian-distribution approach</description>
    <requirements>
        <requirement type="package" version="0.0.1.1">blockbuster</requirement>
    </requirements>
    <command>

            -minClusterHeight $minClusterHeight
            -minBlockHeight $minBlockHeight
            -scale $scale
            -merge $merge
            -tagFilter $tagFilter
            #if str($print).endswith( 'blocks' )
                -print 1
            #else 
                -print 2
            #end if
            $input
            > data.blockbuster;
            #if str($print) == 'bed_blocks'
                awk '{if ($1 ~ /^>/) print $2"\t"$3"\t"$4"\t"$1"\t"$6"\t"$5"\t"$3"\t"$4; else print $2"\t"$3"\t"$4"\tblock_"$1"\t"$6"\t"$5"\t"$3"\t"$4}' data.blockbuster > $output
            #else if str($print) == 'bed_reads'
                awk '{if ($1 ~ /^>/) print $2"\t"$3"\t"$4"\t"$1"\t"$6"\t"$5"\t"$3"\t"$4; else print $1"\t"$2"\t"$3"\t"$3"\t"$4"\t"$5"\t"$6"\t"$2"\t"$3}' data.blockbuster > $output
            #else
                mv data.blockbuster $output
            #end if
]]>
    </command>
    <inputs>
        <param name="input" type="data" format="bed" label="BED file containing read expressions"/>
        <param name="distance" type="integer" value="40" label="minimum distance between two clusters"/>

        <param name="minBlockHeight" type="float" value="1" label="minimum height (readno) of a block"/>
        <param name="scale" type="float" value="0.5" label="scale stddev for a single read"/>
        <param name="merge" type="integer" value="0" label="merge reads with almost similar means"/>
        <param name="tagFilter" type="integer" value="0" label="skip tags with expression smaller than this value"/>
        <param name="print" type="select" label="Type of output" >
            <option value="bbf_blocks">blocks (blockbuster format)</option>
            <option value="bbf_reads" selected="True">reads (blockbuster format)</option>
            <option value="bed_blocks">blocks (bed format)</option>
            <option value="bed_reads" >reads (bed format)</option>
        </param>
    </inputs>

    <outputs>
        <data format="bed" name="output" label="blockbuster on ${on_string}">
            <change_format>
                <when input="print" value="bbf_blocks" format="tabular" />
                <when input="print" value="bbf_reads" format="tabular" />
            </change_format>
	</data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="blockbuster_test_input.bed" ftype="bed" />
            <param name="print" value="bed_blocks" />
            <output name="output" file="blockbuster_test_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="blockbuster_test_input.bed" ftype="bed" />
            <param name="print" value="bbf_blocks" />
            <output name="output" file="blockbuster_test_result2.blockbuster" ftype="tabular" />
        </test>
    </tests>
    <help>
<![CDATA[

**What it does**