Mercurial > repos > iuc > heinz
comparison heinz.xml @ 1:5f589c91566e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author | iuc |
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date | Tue, 30 Oct 2018 18:57:02 -0400 |
parents | e41ec5af7472 |
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0:e41ec5af7472 | 1:5f589c91566e |
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2 <description>using Heinz</description> | 2 <description>using Heinz</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="2.0">heinz</requirement> | 4 <requirement type="package" version="2.0">heinz</requirement> |
5 </requirements> | 5 </requirements> |
6 <command detect_errors="aggressive"><![CDATA[ | 6 <command detect_errors="aggressive"><![CDATA[ |
7 heinz -m \${GALAXY_SLOTS:-2} -n '$score' -e '$edge' 1> '$subnetwork' | 7 heinz -m \${GALAXY_SLOTS:-2} -n '$score' -e '$edge' > '$subnetwork' |
8 ]]></command> | 8 ]]></command> |
9 <inputs> | 9 <inputs> |
10 <param type="data" name="score" format="txt" label="File containing Heinz scores" | 10 <param name="score" type="data" format="txt" label="File containing Heinz scores" |
11 help="The file should contain two columns: the node identifier (e.g. gene) and the corresponding Heinz score" /> | 11 help="The file should contain two columns: the node identifier (e.g. gene) and the corresponding Heinz score" /> |
12 <param type="data" name="edge" format="txt" label="Edge file" | 12 <param name="edge" type="data" format="txt" label="Edge file" |
13 help="In this file, two nodes define one edge, one edge per line" /> | 13 help="In this file, two nodes define one edge, one edge per line" /> |
14 </inputs> | 14 </inputs> |
15 <outputs> | 15 <outputs> |
16 <data name="subnetwork" format="txt" label="${tool.name} on ${on_string}: Optimal subgraph" /> | 16 <data name="subnetwork" format="txt" label="${tool.name} on ${on_string}: Optimal subgraph" /> |
17 </outputs> | 17 </outputs> |
18 <tests> | 18 <tests> |
41 Score file --- the output file of the tool "Calculate Heinz scores": two columns delimited | 41 Score file --- the output file of the tool "Calculate Heinz scores": two columns delimited |
42 by a tab without headers, the first column is node identifier (e.g., genes, KEGG ORTHOLOGY (KO)); | 42 by a tab without headers, the first column is node identifier (e.g., genes, KEGG ORTHOLOGY (KO)); |
43 the second, Heinz score. | 43 the second, Heinz score. |
44 | 44 |
45 ========= =================== | 45 ========= =================== |
46 BRCA2 -6.991782933819368 | 46 BRCA2 -6.991782933819368 |
47 --------- ------------------- | 47 --------- ------------------- |
48 BRCA1 -5.206139799106934 | 48 BRCA1 -5.206139799106934 |
49 --------- ------------------- | 49 --------- ------------------- |
50 AACS -0.9299868303078357 | 50 AACS -0.9299868303078357 |
51 --------- ------------------- | 51 --------- ------------------- |
52 ABCC11 -5.845009850430119 | 52 ABCC11 -5.845009850430119 |
53 ========= =================== | 53 ========= =================== |
54 | |
55 | 54 |
56 Edge file: the background network Heinz uses in the form of a list of edges; each line is made up of | 55 Edge file: the background network Heinz uses in the form of a list of edges; each line is made up of |
57 two node identifiers (e.g., genes, KEGG ORTHOLOGY (KO)) delimited by a tab. In practice, we could | 56 two node identifiers (e.g., genes, KEGG ORTHOLOGY (KO)) delimited by a tab. In practice, we could |
58 prepare this file using different pathway databases, such as Reactome, STRING and KEGG. Which database | 57 prepare this file using different pathway databases, such as Reactome, STRING and KEGG. Which database |
59 to choose depends on the question to solve. | 58 to choose depends on the question to solve. |
65 --------- --------- | 64 --------- --------- |
66 LGALS4 PRKX | 65 LGALS4 PRKX |
67 --------- --------- | 66 --------- --------- |
68 NPTX1 CIAO1 | 67 NPTX1 CIAO1 |
69 ========= ========= | 68 ========= ========= |
70 | |
71 | |
72 ]]></help> | 69 ]]></help> |
73 <citations> | 70 <citations> |
74 <citation type="doi">10.1093/bioinformatics/btn161</citation> | 71 <citation type="doi">10.1093/bioinformatics/btn161</citation> |
75 </citations> | 72 </citations> |
76 </tool> | 73 </tool> |