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comparison teste_out/teste_out.xml @ 0:a3d3dc004a88 draft default tip

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author lucasfsilva
date Thu, 12 Mar 2015 16:36:22 -0400
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1 <tool id="teste_out" name="teste_out" version="0.01">
2 <description>teste_tools_lucas</description>
3
4 <command interpreter="python">
5
6 teste_out.py --script_path "$runMe" --interpreter "python"
7 --tool_name "teste_out"
8
9
10 --input_formats None
11 #for intab in $input1:
12 --input_tab "${intab},${intab.name}"
13 #end for
14
15 --output_dir "./" --output_tab "$output1"
16
17 </command>
18 <inputs>
19 <param name="input_tab" multiple="true" type="data" format="None" label="Select one or more None input files from your history"
20 help="Multiple inputs may be selected assuming the script can deal with them..."/>
21 <param name="job_name" type="text" size="60" label="Supply a name for the outputs to remind you what they contain" value="teste_out"/>
22
23
24 </inputs>
25 <outputs>
26 <data format="txt" name="output1" label="${job_name}"/>
27
28 </outputs>
29 <configfiles>
30 <configfile name="runMe">
31 import sys
32 import os
33 import argparse
34
35 argp=argparse.ArgumentParser()
36 argp.add_argument('--innames',default=None)
37 argp.add_argument('--inpaths',default=None)
38 argp.add_argument('--outpath',default=None)
39 argp.add_argument('--case_sensitive',default=0)
40 argp.add_argument('--additional_parameters',default=[],action="append")
41 argp.add_argument('otherargs', nargs=argparse.REMAINDER)
42 args = argp.parse_args()
43
44
45 f= open(args.outpath,'w')
46 if args.case_sensitive == 0:
47 f.write('teste:\t'.join(args.innames.split(",")).upper())
48 else:
49 f.write('teste:\t'.join(args.innames.split(",")))
50 f.close()
51 </configfile>
52 </configfiles>
53 <tests>
54
55 <test>
56 <param name="input_tab" value="dataset_20.dat,dataset_22.dat" />
57 <param name="job_name" value="test1"/>
58 <param name="runMe" value="$runMe"/>
59 <output name="output1="teste_out_test1_output.xls" ftype="tabular"/>
60
61 </test>
62
63 </tests>
64 <help>
65
66
67 **What it Does**
68 teste
69
70 **Script**
71 Pressing execute will run the following code over your input file and generate some outputs in your history::
72
73
74 import sys
75 import os
76 import argparse
77
78 argp=argparse.ArgumentParser()
79 argp.add_argument('--innames',default=None)
80 argp.add_argument('--inpaths',default=None)
81 argp.add_argument('--outpath',default=None)
82 argp.add_argument('--case_sensitive',default=0)
83 argp.add_argument('--additional_parameters',default=[],action="append")
84 argp.add_argument('otherargs', nargs=argparse.REMAINDER)
85 args = argp.parse_args()
86
87
88 f= open(args.outpath,'w')
89 if args.case_sensitive == 0:
90 f.write('teste:\t'.join(args.innames.split(",")).upper())
91 else:
92 f.write('teste:\t'.join(args.innames.split(",")))
93 f.close()
94
95 **Attribution**
96 This Galaxy tool was created by bioinfolucas@gmail.com at 12/03/2015 17:34:22
97 using the Galaxy Tool Factory.
98
99 See https://bitbucket.org/fubar/galaxytoolfactory for details of that project
100 Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team.
101 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
102
103
104 This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2
105 https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2
106 </help>
107 <citations>
108
109 <citation type="doi">10.1093/bioinformatics/bts573</citation>
110 </citations>
111 </tool>