annotate experimental_design.xml @ 3:beaa487ecf43 draft

Uploaded
author davidvanzessen
date Wed, 07 Dec 2016 08:36:23 -0500
parents afe85eb6572e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
1 <tool id="experimentaldesign_igg" name="ExperimentalDesign" version="1.0">
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
2 <description> </description>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
3 <command interpreter="bash">
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
4 experimental_design/experimental_design.sh
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
5 #for $i, $f in enumerate($patients)
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
6 "$f.id"
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
7 #for $j, $g in enumerate($f.samples)
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
8 ${g.sample}
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
9 #end for
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
10 #end for
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
11 $out_file
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
12 </command>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
13 <inputs>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
14 <repeat name="patients" title="Patient" min="1" default="1">
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
15 <repeat name="samples" title="Sample" min="1" default="1">
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
16 <param name="sample" format="tabular" type="data" label="Sample to Process" />
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
17 </repeat>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
18 <param name="id" type="text" label="ID" />
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
19 </repeat>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
20 </inputs>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
21 <outputs>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
22 <data format="tabular" name="out_file"/>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
23 </outputs>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
24 <help>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
25 Takes the ARGalaxy proprietary format and merges several samples and/or patients together.
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
26 </help>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
27 <citations>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
28 <!-- Example of annotating a citation using a DOI. -->
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
29 <citation type="doi">10.1093/bioinformatics/btq281</citation>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
30
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
31 <!-- Example of annotating a citation using a BibTex entry. -->
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
32 <citation type="bibtex">@ARTICLE{Kim07aninterior-point,
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
33 author = {Seung-jean Kim and Kwangmoo Koh and Michael Lustig and Stephen Boyd and Dimitry Gorinevsky},
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
34 title = {An interior-point method for large-scale l1-regularized logistic regression},
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
35 journal = {Journal of Machine Learning Research},
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
36 year = {2007},
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
37 volume = {8},
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
38 pages = {1519-1555}
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
39 }</citation>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
40 </citations>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
41 <tests>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
42 <test>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
43 <param name="input" value="1.bed"/>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
44 <param name="column" value="1"/>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
45 <param name="order" value="ASC"/>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
46 <param name="style" value="num"/>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
47 <output name="out_file1" file="sort1_num.bed"/>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
48 </test>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
49 <test>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
50 <param name="input" value="7.bed"/>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
51 <param name="column" value="1"/>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
52 <param name="order" value="ASC"/>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
53 <param name="style" value="alpha"/>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
54 <output name="out_file1" file="sort1_alpha.bed"/>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
55 </test>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
56 </tests>
afe85eb6572e Uploaded
davidvanzessen
parents:
diff changeset
57 </tool>