Mercurial > repos > bgruening > sucos_max_score
comparison sucos_max.xml @ 5:d4c67ced6abc draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
author | bgruening |
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date | Wed, 15 Apr 2020 09:26:07 -0400 |
parents | 85fad59f8168 |
children | 55ac04db36aa |
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4:85fad59f8168 | 5:d4c67ced6abc |
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1 <tool id="sucos_max_score" name="Max SuCOS score" version="0.2.2"> | 1 <tool id="sucos_max_score" name="Max SuCOS score" version="0.2.3"> |
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 #if $filter_field and $filter_value | |
12 --filter-field '$filter_field' --filter-value $filter_value | |
13 #end if | |
11 #for $cluster in $clusters | 14 #for $cluster in $clusters |
12 '$cluster' | 15 '$cluster' |
13 #end for | 16 #end for |
14 ]]></command> | 17 ]]></command> |
15 <inputs> | 18 <inputs> |
16 <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." /> | 19 <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input 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." /> | 20 <param name="clusters" type="data" format="sdf" multiple="true" label="Set of clusters to score against" help="Clusters in SDF format." /> |
21 <param name="filter_field" type="text" label="Filter field" optional="true" | |
22 help="Filter output using this field's values. (e.g. Max_SuCOS_Score or Cum_SuCOS_Score)"> | |
23 <sanitizer> | |
24 <valid initial="string.printable"> | |
25 <remove value="'"/> | |
26 </valid> | |
27 <mapping initial="none"/> | |
28 </sanitizer> | |
29 </param> | |
30 <param name="filter_value" type="float" label="Filter value" optional="true" | |
31 help="Filter out scores less than this value."/> | |
18 </inputs> | 32 </inputs> |
19 <outputs> | 33 <outputs> |
20 <data format="sdf" name="output" label="The scored ligands"/> | 34 <data format="sdf" name="output" label="The scored ligands"/> |
21 </outputs> | 35 </outputs> |
22 <tests> | 36 <tests> |
25 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/> | 39 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/> |
26 <output name="output" ftype="sdf"> | 40 <output name="output" ftype="sdf"> |
27 <assert_contents> | 41 <assert_contents> |
28 <has_text text="Max_SuCOS_Score" /> | 42 <has_text text="Max_SuCOS_Score" /> |
29 <has_text text="Cum_SuCOS_Score" /> | 43 <has_text text="Cum_SuCOS_Score" /> |
44 <has_n_lines n="2224" /> | |
45 </assert_contents> | |
46 </output> | |
47 </test> | |
48 <test> | |
49 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/> | |
50 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/> | |
51 <param name="filter_field" value="Cum_SuCOS_Score"/> | |
52 <param name="filter_value" value="15"/> | |
53 <output name="output" ftype="sdf"> | |
54 <assert_contents> | |
55 <has_text text="Max_SuCOS_Score" /> | |
56 <has_text text="Cum_SuCOS_Score" /> | |
57 <has_n_lines n="686" /> | |
30 </assert_contents> | 58 </assert_contents> |
31 </output> | 59 </output> |
32 </test> | 60 </test> |
33 </tests> | 61 </tests> |
34 <help><![CDATA[ | 62 <help><![CDATA[ |
52 **Input** | 80 **Input** |
53 | 81 |
54 The clustered reference compounds are likely to have been generated using the "Cluster ligands using SuCOS" tool and | 82 The clustered reference compounds are likely to have been generated using the "Cluster ligands using SuCOS" tool and |
55 will comprise a SDF format file for each cluster. The ligands to be scored are supplied in a SDF file. | 83 will comprise a SDF format file for each cluster. The ligands to be scored are supplied in a SDF file. |
56 | 84 |
85 Optional filtering of the output is possible, for instance to retain only records with SuCOS scores greater that a | |
86 certain value. Use the optional 'Filter field' and 'Filter value' parameters. The 'Filter field' would typically | |
87 be one of the properties listed below. | |
88 | |
57 .. class:: infomark | 89 .. class:: infomark |
58 | 90 |
59 **Output** | 91 **Output** |
60 | 92 |
61 The same SD file as the input ligands with the following properties added: | 93 The same SD file as the input ligands with the following properties added: |