Mercurial > repos > bgruening > sucos_max_score
comparison sucos_max.xml @ 2:2f110aef9b53 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
author | bgruening |
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date | Thu, 19 Mar 2020 09:43:31 -0400 |
parents | 8eab6d2b7bdf |
children | bf99565cec1f |
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1:8eab6d2b7bdf | 2:2f110aef9b53 |
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1 <tool id="sucos_max_score" name="Max SuCOS score" version="0.1.1"> | 1 <tool id="sucos_max_score" name="Max SuCOS score" version="0.2.0"> |
2 <description>- determine maximum SuCOS score of ligands against clustered fragment hits</description> | 2 <description>- determine maximum SuCOS score of ligands against clustered fragment hits</description> |
3 <macros> | 3 <macros> |
4 <import>sucos_macros.xml</import> | 4 <import>sucos_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 python '$__tool_directory__/sucos_max.py' | 8 python '$__tool_directory__/sucos_max.py' |
9 -i '$input' | 9 -i '$input' |
10 -o '$output' | 10 -o '$output' |
11 -m $mode | |
12 #for $cluster in $clusters | 11 #for $cluster in $clusters |
13 '$cluster' | 12 '$cluster' |
14 #end for | 13 #end for |
15 ]]></command> | 14 ]]></command> |
16 <inputs> | 15 <inputs> |
17 <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." /> | 16 <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." /> |
18 <param name="clusters" type="data" format="sdf" multiple="true" label="Set of clusters to score against" help="Clusters in SDF format." /> | 17 <param name="clusters" type="data" format="sdf" multiple="true" label="Set of clusters to score against" help="Clusters in SDF format." /> |
19 <param name="mode" type="select" value="max" label="Mode"> | |
20 <option value="max">Max score</option> | |
21 <option value="cum">Cumulative score</option> | |
22 </param> | |
23 </inputs> | 18 </inputs> |
24 <outputs> | 19 <outputs> |
25 <data format="sdf" name="output" label="The scored ligands"/> | 20 <data format="sdf" name="output" label="The scored ligands"/> |
26 </outputs> | 21 </outputs> |
27 <tests> | 22 <tests> |
28 <test> | 23 <test> |
29 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/> | 24 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/> |
30 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/> | 25 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/> |
31 <param name="mode" value="max"/> | |
32 <output name="output" ftype="sdf"> | 26 <output name="output" ftype="sdf"> |
33 <assert_contents> | 27 <assert_contents> |
34 <has_text text="Max_SuCOS_Score" /> | 28 <has_text text="Max_SuCOS_Score" /> |
35 </assert_contents> | |
36 </output> | |
37 </test> | |
38 <test> | |
39 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/> | |
40 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/> | |
41 <param name="mode" value="cum"/> | |
42 <output name="output" ftype="sdf"> | |
43 <assert_contents> | |
44 <has_text text="Cum_SuCOS_Score" /> | 29 <has_text text="Cum_SuCOS_Score" /> |
45 </assert_contents> | 30 </assert_contents> |
46 </output> | 31 </output> |
47 </test> | 32 </test> |
48 </tests> | 33 </tests> |
71 | 56 |
72 .. class:: infomark | 57 .. class:: infomark |
73 | 58 |
74 **Output** | 59 **Output** |
75 | 60 |
76 The same SD file as the input ligands with a "Max_SuCOS_Score" property added containing the best (maximum) SuCOS score | 61 The same SD file as the input ligands with the following properties added: |
77 along with the "Max_SuCOS_FeatureMap_Score" and "Max_SuCOS_Tanimoto_Score" of that comparison. | |
78 | 62 |
79 In addition, the "Max_SuCOS_Cluster" field shows the name of the cluster file that contained the molecule with this best | 63 * Max_SuCOS_Score - the best (maximum) SuCOS score |
80 score and the "Max_SuCOS_Index" shows the index (first record is index 1) of that molecule in the file. | 64 * Max_SuCOS_FeatureMap_Score - the corresponding FeatureMap score |
65 * Max_SuCOS_Protrude_Score - the corresponding Protrude score | |
66 * Max_SuCOS_Cluster - the file name of the cluster that contained the max score | |
67 * Max_SuCOS_Index - the index of the cluster that contained the max score (first record is index 1) | |
68 * Cum_SuCOS_Score - the cumulative SuCOS score for all overlays (the sum of the individual scores) | |
69 * Cum_SuCOS_FeatureMap_Score - the corresponding FeatureMap score | |
70 * Cum_SuCOS_Protrude_Score - the corresponding Protrude score | |
81 | 71 |
82 ]]></help> | 72 ]]></help> |
83 <expand macro="citations"/> | 73 <expand macro="citations"/> |
84 </tool> | 74 </tool> |
85 | 75 |