Mercurial > repos > stemcellcommons > scdetools
comparison scde_list_compare.xml @ 0:b1d730728d5f default tip
Initial commit.
author | Ilya Sytchev <isytchev@hsph.harvard.edu> |
---|---|
date | Mon, 07 Oct 2013 18:54:25 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:b1d730728d5f |
---|---|
1 <tool id="scde-list-compare" name="SCDE ListCompare" version="1.0" hidden="false"> | |
2 <description>compare multiple lists against one or more selected reference lists</description> | |
3 <version_string>scde --version</version_string> | |
4 | |
5 <command interpreter="perl"> | |
6 scde compare --source $source | |
7 | |
8 #for $i in $lists | |
9 --file ${i.filename} | |
10 --column ${i.column} | |
11 --organism ${i.organism} | |
12 --symbol ${i.symbol_type} | |
13 #end for | |
14 --output $format | |
15 | |
16 #if str($output_html) != "None" | |
17 > $output_html | |
18 #else | |
19 > $output_tab | |
20 #end if | |
21 </command> | |
22 | |
23 <inputs> | |
24 <param name="source" type="select" label="Compare your gene lists to"> | |
25 <option value="wikipathways">Wikipathways</option> | |
26 <option value="genesigdb">GeneSigDB</option> | |
27 <option value="msigdb">MSigDB</option> | |
28 <option value="scd">SCDE Repository - Public</option> | |
29 </param> | |
30 | |
31 <repeat name="lists" title="Add List" min="2" > | |
32 <param name="filename" type="data" format="txt" label="Dataset" help="Select a list for comparison from your History." /> | |
33 | |
34 <param name="column" type="select" label="Gene Column" help="Select the column number corresponding to the gene identifier"> | |
35 <option value="1">c1</option> | |
36 <option value="2">c2</option> | |
37 <option value="3">c3</option> | |
38 <option value="4">c4</option> | |
39 <option value="5">c5</option> | |
40 <option value="6">c6</option> | |
41 <option value="7">c7</option> | |
42 <option value="8">c8</option> | |
43 <option value="9">c9</option> | |
44 <option value="10">c10</option> | |
45 </param> | |
46 | |
47 <param name="organism" type="select" label="Query Organism" help="Which organism do your gene lists come from?"> | |
48 <option value="human">Human</option> | |
49 <option value="mouse">Mouse</option> | |
50 </param> | |
51 | |
52 <param name="symbol_type" type="select" label="Query Gene ID Type" help="Select the gene identifier type to search with."> | |
53 <option value="symbol">Gene Symbol</option> | |
54 <option value="ensembl">Ensembl ID</option> | |
55 <option value="entrez">Entrez ID</option> | |
56 </param> | |
57 </repeat> | |
58 | |
59 <param name="format" type="select" label="Output Format" help="Select the Format for the Output File"> | |
60 <option value="html">HTML</option> | |
61 <option value="tab">Tab Delimited</option> | |
62 </param> | |
63 </inputs> | |
64 | |
65 <outputs> | |
66 <data format="html" name="output_html"> | |
67 <filter>format == "html"</filter> | |
68 </data> | |
69 <data format="tabular" name="output_tab"> | |
70 <filter>format == "tab"</filter> | |
71 </data> | |
72 </outputs> | |
73 | |
74 <help> | |
75 **What it does** | |
76 | |
77 This tool compares two or more sets of gene lists against one or more selected reference lists. | |
78 | |
79 ----- | |
80 | |
81 .. class:: infomark | |
82 | |
83 Upload data in tabular format to your history using the "Get Data" -> "Upload File" tool. | |
84 | |
85 .. class:: infomark | |
86 | |
87 Additional lists may be added using the "Add new List" button. | |
88 </help> | |
89 </tool> | |
90 |