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annotate chemfp_clustering/nxn_clustering.xml @ 0:a8ac5250d59c

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author bgruening
date Tue, 26 Mar 2013 13:05:41 -0400
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1 <tool id="chemfp_nxn_clustering" name="NxN Clustering" version="0.1">
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2 <description>of molecular libraries</description>
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3 <requirements>
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4 <requirement type="package" version="1.7.0">numpy</requirement>
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5 <requirement type="package" version="1.1p1">chemfp</requirement>
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6 </requirements>
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7 <command interpreter='python'>
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8 nxn_clustering.py $infile $threshold $outfile
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9 </command>
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10 <inputs>
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11 <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
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12 <param name='threshold' type='float' value='0.75' ></param>
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13 </inputs>
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14 <outputs>
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15 <data type="data" format="svg" name="outfile" />
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="infile" ftype="fps" value="q.fps" />
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20 <param value='0.75' />
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21 <output ftype="svg" name="outfile" file='NxN_Clustering_on_q.svg' />
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22 </test>
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23 </tests>
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24 <help>
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25
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26
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27 **What it does**
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28 Generating hierarchical clusters and visualizing clusters with dendrograms.
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29
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30 -----
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31
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32 **Example**
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33
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34 * input::
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35
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36 - fingerprints in FPS format
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37
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38 #FPS1
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39 #num_bits=881
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40 #type=CACTVS-E_SCREEN/1.0 extended=2
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41 #software=CACTVS/unknown
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42 #source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat
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43 #date=2012-02-09T13:20:37
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44 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e
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45 19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000 55169009
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46 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e
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47 19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000 55079807
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48 ........
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49
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50 - Tanimoto threshold : 0.8 (between 0 and 1)
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51
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52 * output::
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53
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54 plot for the clustring
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55
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56 .. image:: ./static/images/chemfpclustoutput.svg
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57
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58
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59 </help>
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60
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61 </tool>