Mercurial > repos > ambarishk > mytoolshed
comparison tool1/tool1.xml @ 0:9cc0f9a8912e draft default tip
Uploaded
author | ambarishk |
---|---|
date | Thu, 21 Apr 2016 06:45:57 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:9cc0f9a8912e |
---|---|
1 <tool id="tool1" name="tool1" version="0.01"> | |
2 <description>grep command</description> | |
3 | |
4 <command interpreter="python"> | |
5 | |
6 tool1.py --script_path "$runMe" --interpreter "python" | |
7 --tool_name "tool1" | |
8 | |
9 --output_dir "./" --output_tab "$output1" | |
10 | |
11 </command> | |
12 <inputs> | |
13 <param name="job_name" type="text" size="60" label="Supply a name for the outputs to remind you what they contain" value="tool1"/> | |
14 | |
15 | |
16 </inputs> | |
17 <outputs> | |
18 <data format="ab1" name="output1" label="${job_name}"/> | |
19 | |
20 </outputs> | |
21 <configfiles> | |
22 <configfile name="runMe"> | |
23 import re | |
24 hand = open('/home/guest/word.txt') | |
25 for line in hand: | |
26 line = line.rstrip() | |
27 if re.search('is', line) : | |
28 print line | |
29 </configfile> | |
30 </configfiles> | |
31 <tests> | |
32 | |
33 <test> | |
34 | |
35 <param name="job_name" value="test1"/> | |
36 <param name="runMe" value="$runMe"/> | |
37 <output name="output1="tool1_test1_output.xls" ftype="tabular"/> | |
38 | |
39 </test> | |
40 | |
41 </tests> | |
42 <help> | |
43 | |
44 | |
45 get the line. | |
46 | |
47 **Script** | |
48 Pressing execute will run the following code over your input file and generate some outputs in your history:: | |
49 | |
50 | |
51 import re | |
52 hand = open('/home/guest/word.txt') | |
53 for line in hand: | |
54 line = line.rstrip() | |
55 if re.search('is', line) : | |
56 print line | |
57 | |
58 **Attribution** | |
59 This Galaxy tool was created by admin@ngsap.com at 13/04/2016 19:49:50 | |
60 using the Galaxy Tool Factory. | |
61 | |
62 See https://bitbucket.org/fubar/galaxytoolfactory for details of that project | |
63 Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. | |
64 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 | |
65 | |
66 | |
67 This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2 | |
68 https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2 | |
69 </help> | |
70 <citations> | |
71 | |
72 <citation type="doi">10.1093/bioinformatics/bts573</citation> | |
73 </citations> | |
74 </tool> |