Mercurial > repos > bgruening > chemfp
annotate chemfp_clustering/nxn_clustering.xml @ 1:43a9e7d9b24f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
| author | bgruening |
|---|---|
| date | Sun, 01 Nov 2015 10:27:01 -0500 |
| parents | 354d3c6bb894 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="ctb_chemfp_nxn_clustering" name="NxN Clustering" version="0.2"> |
| 2 <description>of molecular fingerprints</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.7.0">numpy</requirement> | |
| 5 <requirement type="package" version="1.1p1">chemfp</requirement> | |
| 6 <requirement type="package" version="1.2.1">matplotlib</requirement> | |
| 7 <requirement type="package" version="0.12.0">scipy</requirement> | |
| 8 <requirement type="package" version="2.3.2">openbabel</requirement> | |
| 9 </requirements> | |
| 10 <command interpreter='python'> | |
|
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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11 <![CDATA[ |
| 0 | 12 nxn_clustering.py |
| 13 -i $infile | |
| 14 -t $threshold | |
| 15 #if str($output_files) in ['both', 'image']: | |
| 16 --cluster $image | |
| 17 #end if | |
| 18 #if str($output_files) in ['both', 'matrix']: | |
| 19 --smatrix $smilarity_matrix | |
| 20 #end if | |
| 21 --oformat $oformat | |
|
1
43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
22 ]]> |
| 0 | 23 </command> |
| 24 <inputs> | |
| 25 <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/> | |
| 26 <param name='threshold' type='float' value='0.0' /> | |
| 27 <param name='oformat' type='select' format='text' label="Format of the resulting picture"> | |
| 28 <option value='png'>PNG</option> | |
| 29 <option value='svg'>SVG</option> | |
| 30 </param> | |
| 31 <param name='output_files' type='select' format='text' label="Output options"> | |
| 32 <option value='both'>NxN matrix and Image</option> | |
| 33 <option value='image'>Image</option> | |
| 34 <option value='matrix'>NxN Matrix</option> | |
| 35 </param> | |
| 36 | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data name="image" type="data" format="svg" label="${tool.name} on ${on_string} - Cluster Image"> | |
| 40 <filter>output_files == "both" or output_files == "image"</filter> | |
| 41 <change_format> | |
| 42 <when input="oformat" value="png" format="png"/> | |
| 43 </change_format> | |
| 44 </data> | |
| 45 <data name="smilarity_matrix" format="binary" label="${tool.name} on ${on_string} - Similarity Matrix"> | |
| 46 <filter>output_files == "both" or output_files == "matrix"</filter> | |
| 47 </data> | |
| 48 </outputs> | |
| 49 <tests> | |
| 50 <test> | |
| 51 <param name="infile" ftype="fps" value="q.fps" /> | |
| 52 <param name='treshold' value='0.75' /> | |
| 53 <param name='output_files' value='image' /> | |
| 54 <output ftype="svg" name="outfile" file='NxN_Clustering_on_q.svg' /> | |
| 55 </test> | |
| 56 </tests> | |
| 57 <help> | |
|
1
43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
58 <![CDATA[ |
| 0 | 59 |
| 60 .. class:: infomark | |
| 61 | |
| 62 **What this tool does** | |
| 63 | |
| 64 Generating hierarchical clusters and visualizing clusters with dendrograms. | |
| 65 For the clustering and the fingerprint handling the chemfp_ project is used. | |
| 66 | |
| 67 .. _chemfp: http://chemfp.com/ | |
| 68 | |
| 69 ----- | |
| 70 | |
| 71 .. class:: warningmark | |
| 72 | |
| 73 **Hint** | |
| 74 | |
| 75 The plotting of the cluster image is sensible only with a small dataset. | |
| 76 | |
| 77 ----- | |
| 78 | |
| 79 .. class:: infomark | |
| 80 | |
| 81 **Input** | |
| 82 | |
| 83 Molecular fingerprints in FPS format. Open Babel Fastsearch index is not supported. | |
| 84 | |
| 85 * Example:: | |
| 86 | |
| 87 - fingerprints in FPS format | |
| 88 | |
| 89 #FPS1 | |
| 90 #num_bits=881 | |
| 91 #type=CACTVS-E_SCREEN/1.0 extended=2 | |
| 92 #software=CACTVS/unknown | |
| 93 #source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat | |
| 94 #date=2012-02-09T13:20:37 | |
| 95 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e | |
| 96 19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000 55169009 | |
| 97 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e | |
| 98 19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000 55079807 | |
| 99 ........ | |
| 100 | |
| 101 - Tanimoto threshold : 0.8 (between 0 and 1) | |
| 102 | |
| 103 ----- | |
| 104 | |
| 105 .. class:: informark | |
| 106 | |
| 107 **Output** | |
| 108 | |
| 109 * Example:: | |
| 110 | |
| 111 .. image:: $PATH_TO_IMAGES/NxN_clustering.png | |
| 112 | |
| 113 ----- | |
| 114 | |
| 115 .. class:: infomark | |
| 116 | |
| 117 **Cite** | |
| 118 | |
| 119 The chemfp_ project from Andrew Dalke! | |
| 120 | |
| 121 .. _chemfp: http://chemfp.com/ | |
| 122 | |
|
1
43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
123 ]]> |
| 0 | 124 </help> |
| 125 | |
| 126 </tool> |