Mercurial > repos > bgruening > sucos_max_score

comparison sucos_max.xml @ 2:2f110aef9b53 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
author bgruening
date Thu, 19 Mar 2020 09:43:31 -0400
parents 8eab6d2b7bdf
children bf99565cec1f
comparison
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1:8eab6d2b7bdf 2:2f110aef9b53
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