diff chemfp_clustering/nxn_clustering.xml @ 0:354d3c6bb894 draft

Uploaded

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+++ b/chemfp_clustering/nxn_clustering.xml	Thu Aug 15 03:27:06 2013 -0400
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+<tool id="ctb_chemfp_nxn_clustering" name="NxN Clustering" version="0.2">
+    <description>of molecular fingerprints</description>
+    <requirements>
+        <requirement type="package" version="1.7.0">numpy</requirement>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+        <requirement type="package" version="1.2.1">matplotlib</requirement>
+        <requirement type="package" version="0.12.0">scipy</requirement>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command interpreter='python'>
+        nxn_clustering.py
+            -i $infile
+            -t $threshold
+            #if str($output_files) in ['both', 'image']:
+                --cluster $image
+            #end if
+            #if str($output_files) in ['both', 'matrix']:
+                --smatrix $smilarity_matrix
+            #end if
+            --oformat $oformat
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
+        <param name='threshold' type='float' value='0.0' />
+        <param name='oformat' type='select' format='text' label="Format of the resulting picture">
+            <option value='png'>PNG</option>
+            <option value='svg'>SVG</option>
+        </param>
+        <param name='output_files' type='select' format='text' label="Output options">
+            <option value='both'>NxN matrix and Image</option>
+            <option value='image'>Image</option>
+            <option value='matrix'>NxN Matrix</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="image" type="data" format="svg" label="${tool.name} on ${on_string} - Cluster Image">
+            <filter>output_files == "both" or output_files == "image"</filter>
+            <change_format>
+                <when input="oformat" value="png" format="png"/>
+            </change_format>
+        </data>
+        <data name="smilarity_matrix" format="binary" label="${tool.name} on ${on_string} - Similarity Matrix">
+            <filter>output_files == "both" or output_files == "matrix"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="fps" value="q.fps" />
+            <param name='treshold' value='0.75' />
+            <param name='output_files' value='image' />
+            <output ftype="svg" name="outfile" file='NxN_Clustering_on_q.svg' />
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What this tool does**
+
+Generating hierarchical clusters and visualizing clusters with dendrograms.
+For the clustering and the fingerprint handling the chemfp_ project is used.
+
+.. _chemfp: http://chemfp.com/
+
+-----
+
+.. class:: warningmark
+
+**Hint**
+
+The plotting of the cluster image is sensible only with a small dataset.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+Molecular fingerprints in FPS format. Open Babel Fastsearch index is not supported.
+
+* Example::
+
+	-  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)
+
+-----
+
+.. class:: informark
+
+**Output**
+
+* Example::
+
+	.. image:: $PATH_TO_IMAGES/NxN_clustering.png
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+The chemfp_ project from Andrew Dalke!
+
+.. _chemfp: http://chemfp.com/
+
+    </help>
+
+</tool>