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comparison countmatrixforedger.xml @ 0:c5a812cdf478 draft

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author marpiech
date Fri, 09 Dec 2016 10:52:35 -0500
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-1:000000000000 0:c5a812cdf478
1 <tool id="countmatrixforedger" name="countMatrixForEdger" version="1.0">
2 <description>Make a count matrix for edgeR</description>
3 <stdio>
4 <exit_code range="1:" />
5 </stdio>
6 <command>
7 <![CDATA[
8 #for $i, $s in enumerate( $sample )#
9 echo -e ${s.sample_data}"\t"${s.sample_name}"\t"${s.sample_group} >> script.data;
10 #end for#
11
12 cat script.data > /tmp/script.data;
13 $__tool_directory__/tools/scrsh.sh script.data;
14
15 cat count.matrix > $count_matrix;
16 cat annotation > $annotation;
17 cat script.log > $log;
18 cat error.log > $error_log
19
20 ]]>
21 </command>
22 <inputs>
23 <repeat name="sample" title="">
24 <param name="sample_data" type="data" format="data" label="" help="" />
25 <param name="sample_name" type="text" label="" help="" />
26 <param name="sample_group" type="text" label="" help="" />
27 </repeat>
28 </inputs>
29 <outputs>
30 <!-- <data name="output" format="data" /> -->
31 <data name="count_matrix" format="data" />
32 <data name="annotation" format="data" />
33 <data name="log" format="data" />
34 <data name="error_log" format="data" />
35 </outputs>
36 <tests>
37 <!-- <test>
38 <param name="sample_0|sample_data" value="data1" />
39 <param name="sample_1|sample_data" value="data2" />
40 <param name="sample_2|sample_data" value="data3" />
41 <param name="sample_3|sample_data" value="data4" />
42 <param name="sample_0|sample_name" value="sample1" />
43 <param name="sample_1|sample_name" value="sample2" />
44 <param name="sample_2|sample_name" value="sample3" />
45 <param name="sample_3|sample_name" value="sample4" />
46 <param name="sample_0|sample_group" value="gr1" />
47 <param name="sample_1|sample_group" value="gr1" />
48 <param name="sample_2|sample_group" value="gr2" />
49 <param name="sample_3|sample_group" value="gr2" />
50 <output name="output" file="output"/>
51
52 </test> -->
53 <test>
54 <param name="sample_0|sample_data" value="data1" />
55 <param name="sample_1|sample_data" value="data2" />
56 <param name="sample_2|sample_data" value="data3" />
57 <param name="sample_3|sample_data" value="data4" />
58 <param name="sample_0|sample_name" value="sample1" />
59 <param name="sample_1|sample_name" value="sample2" />
60 <param name="sample_2|sample_name" value="sample3" />
61 <param name="sample_3|sample_name" value="sample4" />
62 <param name="sample_0|sample_group" value="gr1" />
63 <param name="sample_1|sample_group" value="gr1" />
64 <param name="sample_2|sample_group" value="gr2" />
65 <param name="sample_3|sample_group" value="gr2" />
66 <output name="count_matrix" file="count.matrix"/>
67 <output name="annotation" file="annotation"/>
68 <output name="log" file="script.log"/>
69 <output name="error_log" file="error.log"/>
70 </test>
71
72 </tests>
73 <help>
74 <![CDATA[
75
76 tutaj cos bedzie
77 ]]>
78 </help>
79 <citations>
80 <citation type="bibtex">
81 @article{Berenger2014,
82 doi = {10.1186/1758-2946-6-23},
83 url = {http://dx.doi.org/10.1186/1758-2946-6-23},
84 year = {2014},
85 publisher = {Springer Nature},
86 volume = {6},
87 number = {1},
88 pages = {23},
89 author = {Francois Berenger and Arnout Voet and Xiao Lee and Kam YJ Zhang},
90 title = {A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening},
91 journal = {Journal of Cheminformatics}
92 }
93 </citation>
94 </citations>
95 </tool>