# HG changeset patch
# User bgruening
# Date 1710247940 0
# Node ID 4d1e4e729ae469da45ae956f4630f01a40b6171e

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

diff -r 000000000000 -r 4d1e4e729ae4 datatypes_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Tue Mar 12 12:52:20 2024 +0000
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<datatypes>
+    <registration>
+        <datatype extension="mcxio" type="galaxy.datatypes.data:Text" mimetype="text/plain" subclass="True" display_in_upload="true" />
+    </registration>
+    <sniffers>
+    </sniffers>
+</datatypes>
diff -r 000000000000 -r 4d1e4e729ae4 mcl.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mcl.xml	Tue Mar 12 12:52:20 2024 +0000
@@ -0,0 +1,92 @@
+<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>
diff -r 000000000000 -r 4d1e4e729ae4 readme.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Tue Mar 12 12:52:20 2024 +0000
@@ -0,0 +1,68 @@
+====================================
+Galaxy wrapper for MCL cluster tools
+====================================
+
+The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs. The algorithm was invented/discovered by Stijn van Dongen (that is, me) at the Centre for Mathematics and Computer Science (also known as CWI) in the Netherlands. The PhD thesis Graph clustering by flow simulation is centered around this algorithm, the main topics being the mathematical theory behind it, its position in cluster analysis and graph clustering, issues concerning scalability, implementation, and benchmarking, and performance criteria for graph clustering in general. The work for this thesis was carried out under supervision of Jan van Eijck and Michiel Hazewinkel. The thesis, technical reports, and preprints can be found in this section. For quickly getting an idea of how MCL operates, consider the flow pictorial at the top of this page, or even better, have a look at an animation of the MCL process. 
+
+This wrapper is copyright 2013 by:
+ * Bjoern Gruening
+ * Pavan Videm
+
+
+This prepository contains wrapper for the MCL_ command line tool.
+
+.. _MCL: http://micans.org/mcl/
+
+
+
+Stijn van Dongen, Graph Clustering by Flow Simulation, PhD thesis, University of Utrecht, May 2000.
+( http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm )
+
+Stijn van Dongen, A cluster algorithm for graphs, Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam, May 2000.
+( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z )
+
+Stijn van Dongen, Graph clustering via a discrete uncoupling process, Siam Journal on Matrix Analysis and Applications 30-1, p121-141, 2008.
+
+Stijn van Dongen and Cei Abreu-Goodger, Using MCL to extract clusters from networks, in Bacterial Molecular Networks: Methods and Protocols, Methods in Molecular Biology, Vol 804, pages 281—295 (2012). PMID 22144159.
+
+
+
+============
+Installation
+============
+
+MCL will be installed automatically with the Galaxy Tool Shed.
+
+
+
+=======
+History
+=======
+
+interproscan:
+
+ - v0.1: Initial public release of version 12.135
+
+
+===============================
+Wrapper Licence (MIT/BSD style)
+===============================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
+
diff -r 000000000000 -r 4d1e4e729ae4 test-data/mcl_result_01.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mcl_result_01.tabular	Tue Mar 12 12:52:20 2024 +0000
@@ -0,0 +1,2 @@
+cat	hat	bat
+bit	fit	hit
diff -r 000000000000 -r 4d1e4e729ae4 test-data/sample_input.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_input.tabular	Tue Mar 12 12:52:20 2024 +0000
@@ -0,0 +1,7 @@
+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
diff -r 000000000000 -r 4d1e4e729ae4 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Mar 12 12:52:20 2024 +0000
@@ -0,0 +1,6 @@
+<?xml version="1.0" ?>
+<tool_dependency>
+    <package name="mcl" version="12.135">
+        <repository name="package_mcl_12_135" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="9f59d1a59999"/>
+    </package>
+</tool_dependency>
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