diff chemfp_clustering/nxn_clustering.xml @ 0:a8ac5250d59c

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/nxn_clustering.xml	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,61 @@
+<tool id="chemfp_nxn_clustering" name="NxN Clustering" version="0.1">
+    <description>of molecular libraries</description>
+    <requirements>
+        <requirement type="package" version="1.7.0">numpy</requirement>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+    </requirements>
+    <command interpreter='python'>
+        nxn_clustering.py $infile $threshold $outfile
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
+        <param name='threshold' type='float' value='0.75' ></param>
+    </inputs>
+    <outputs>
+        <data type="data" format="svg" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="fps" value="q.fps" />
+            <param value='0.75' />
+            <output ftype="svg" name="outfile" file='NxN_Clustering_on_q.svg' />
+        </test>
+    </tests>
+    <help>
+
+
+**What it does**
+Generating hierarchical clusters and visualizing clusters with dendrograms.
+
+-----
+
+**Example**
+
+* input::
+
+	-  fingerprints in FPS format
+
+		#FPS1
+		#num_bits=881
+		#type=CACTVS-E_SCREEN/1.0 extended=2
+		#software=CACTVS/unknown
+		#source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat
+		#date=2012-02-09T13:20:37
+		07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e
+		19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000	55169009
+		07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e
+		19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000	55079807
+		........
+
+	- Tanimoto threshold : 0.8 (between 0 and 1)
+
+* output::
+
+	plot for the clustring
+
+.. image:: ./static/images/chemfpclustoutput.svg
+
+ 
+    </help>
+
+</tool>