diff mcl.xml @ 0:4d1e4e729ae4 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mcl commit dcb4abd1fcf9114ced686c7343c2de4b064a57c1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mcl.xml	Tue Mar 12 12:52:20 2024 +0000
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+<tool id="mcl_clustering" name="MCL"  version="14.137">
+    <description>A Markov Cluster Algorithm.</description>
+    <xrefs>
+        <xref type="bio.tools">mcl</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="14.137">mcl</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+<![CDATA[
+    mcl
+        $infile
+        --abc
+        -I $inflation
+        -o $outfile
+        -scheme $scheme
+        -pi $pi
+        -ph $ph
+        -if $if
+        --discard-loops=$discard_loops
+]]>
+    </command>
+        <inputs>
+            <param name="infile" type="data" format="tabular" label="MCL Label input"/>
+
+            <param name="inflation" type="float" value="4.0" label="Main inflation value (-I)"
+                help="This value is the main handle for affecting cluster granularity. It is usually chosen somewhere in the range [1.2-5.0]. -I 5.0 will tend to result in fine-grained clusterings, and -I 1.2 will tend to result in very coarse grained clusterings."/>
+            <param name="pi" type="float" label="pre-inflation (-pi)" value="3.0" help=""/>
+            <param name="ph" type="float" label="pre-inflation, max-bound (-ph)" value="3.0" help=""/>
+            <param name="if" type="float" label="start-inflation (-if)" value="3.0" help=""/>
+
+            <param name="discard_loops" truevalue="y" falsevalue="n" checked="True" type="boolean"
+                label="remove any loops that are present in the input" help=""/>
+
+            <param name="scheme" type="select" label="Resource schemes (-scheme)"
+                help="High schemes result in more expensive computations that may possibly be more accurate.">
+                <option value="1">1</option>
+                <option value="2">2</option>
+                <option value="3">3</option>
+                <option value="4" selected="true">4</option>
+                <option value="5">5</option>
+                <option value="6">6</option>
+                <option value="7">7</option>
+            </param>
+
+        </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="MCS on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="sample_input.tabular" ftype="tabular" />
+            <param name="inflation" value="2.0" />
+            <param name="scheme" value="4" />
+            <output name="outfile" file="mcl_result_01.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+**What it does**
+
+The Markov Cluster Algorithm, aka the MCL algorithm.
+
+This program implements mcl, a cluster algorithm for graphs.
+A single parameter controls the granularity of the output clustering, namely the -I inflation option described further below.
+In standard usage of the program this parameter is the only one that may require changing.
+By default it is set to 2.0 and this is a good way to start. If you want to explore cluster structure in graphs with MCL,
+vary this parameter to obtain clusterings at different levels of granularity. A good set of starting values is 1.4, 2, 4, and 6.
+
+**Example input (Label input)**
+
+::
+
+    cat hat 0.2
+    hat bat 0.16
+    bat cat 1.0
+    bat bit 0.125
+    bit fit 0.25
+    fit hit 0.5
+    hit bit 0.16
+
+]]>
+    </help>
+    <creator>
+        <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening" />
+        <person givenName="Pavankumar" familyName="Videm" url="https://github.com/pavanvidem" />
+    </creator>
+    <citations>
+        <citation type="doi">10.1137/040608635</citation>
+    </citations>
+</tool>