Mercurial > repos > earlhaminst > hcluster_sg

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hcluster_sg.xml	Fri Nov 11 06:56:10 2016 -0500
@@ -0,0 +1,69 @@
+<tool id="hcluster_sg" name="hcluster_sg" version="0.5.1">
+    <description>Hierarchically clustering on a sparse graph</description>
+    <requirements>
+        <requirement type="package" version="0.5.1">hcluster_sg</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+hcluster_sg
+-w $w
+-s $s
+-m $m
+$c
+-b $b
+$O.O_selector
+#if $O.O_selector == '-O'
+    -r $O.r
+#end if
+#if $C
+    -C $C
+#end if
+-L $L
+$inputFile
+> $outputFile
+]]>
+    </command>
+    <inputs>
+        <param name="inputFile" type="data" format="tabular" label="Weight file" help="3-columns format: id-1 id-2 integer-weight" />
+        <param name="w" type="integer" min="0" value="20" label="Minimum edge weight" help="(-w)" />
+        <param name="s" type="float" value="0.5" label="Minimum edge density between a join" help="(-s)" />
+        <param name="m" type="integer" value="500" label="Maximum size" help="(-m)" />
+        <param name="c" type="boolean" truevalue="-c" falsevalue="" label="Only find single-linkage clusters" help="Bypass h-cluster (-c)" />
+        <param name="b" type="float" value="0.1" label="Breaking edge density" help="(-b)" />
+        <conditional name="O">
+            <param name="O_selector" type="select" label="Use once-fail-inactive-forever mode" help="(-O)">
+                <option value="-O">Yes</option>
+                <option value="" selected="true">No</option>
+            </param>
+            <when value="-O">
+                <param name="r" type="integer" value="5" label="Weight resolution" help="(-r)" />
+            </when>
+            <when value="" />
+        </conditional>
+        <param name="C" type="data" format="tabular" optional="true" label="Category file" help="(-C)" />
+        <param name="L" type="integer" value="2" label="Stringency level" help="(-L)" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outputFile" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputFile" ftype="tabular" value="exam-1.txt" />
+            <output name="outputFile" file="hcluster_sg1.txt" />
+        </test>
+        <test>
+            <param name="inputFile" ftype="tabular" value="exam-1.txt" />
+            <param name="c" value="true" />
+            <output name="outputFile" file="hcluster_sg2.txt" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Simple wrapper for `hcluster_sg`_.
+
+.. _hcluster_sg: https://github.com/douglasgscofield/hcluster
+]]>
+    </help>
+    <citations>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exam-1.txt	Fri Nov 11 06:56:10 2016 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hcluster_sg1.txt	Fri Nov 11 06:56:10 2016 -0500
@@ -0,0 +1,9 @@
+0	0	57	1.000	0	13	11,0,4,3,5,12,7,10,13,2,1,6,9,
+1	0	23	0.671	0	46	45,39,71,83,49,61,64,38,25,72,44,29,90,35,30,28,62,65,63,88,89,34,82,73,52,74,17,55,41,56,59,51,32,33,87,31,85,27,48,66,50,37,60,77,26,54,
+2	0	0	1.000	0	1	84,
+3	0	33	1.000	0	8	101,96,92,98,94,100,91,99,
+4	0	28	1.000	0	4	40,43,76,42,
+5	0	0	1.000	0	1	8,
+6	0	54	1.000	0	8	18,23,21,15,22,20,14,16,
+7	0	15	0.596	0	17	24,95,58,69,78,36,68,70,57,67,97,79,53,47,75,86,46,
+8	0	0	1.000	0	1	102,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hcluster_sg2.txt	Fri Nov 11 06:56:10 2016 -0500
@@ -0,0 +1,5 @@
+0	99	0,13,39,84,83,96,101,100,99,98,76,43,8,42,40,14,24,86,97,95,102,79,78,75,70,69,68,67,58,57,53,47,46,36,23,22,21,20,18,16,15,94,92,91,90,89,88,87,85,73,41,38,33,27,26,25,17,82,77,74,72,71,66,65,64,63,62,61,60,59,56,55,54,52,51,50,49,48,45,44,34,32,31,37,35,30,29,28,12,11,10,9,7,6,5,4,3,2,1,
+1	1	19,
+2	1	80,
+3	1	81,
+4	1	93,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Nov 11 06:56:10 2016 -0500
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="hcluster_sg" version="0.5.1">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">git clone https://github.com/douglasgscofield/hcluster.git hcluster_sg</action>
+                <action type="shell_command">make</action>
+                <action type="make_directory">$INSTALL_DIR/bin</action>
+                <action type="move_file">
+                    <source>hcluster_sg</source>
+                    <destination>$INSTALL_DIR/bin/</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+hcluster_sg is tool for hierarchically clustering on a sparse graph.
+        </readme>
+    </package>
+</tool_dependency>