Mercurial > repos > davidvanzessen > argalaxy_tools
comparison experimental_design.xml @ 0:f90fbc15b35a draft
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| author | davidvanzessen |
|---|---|
| date | Thu, 16 Jul 2015 08:30:43 -0400 |
| parents | |
| children | c06d0df9ec44 |
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| -1:000000000000 | 0:f90fbc15b35a |
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| 1 <tool id="experimentaldesign_igg" name="ExperimentalDesign" version="1.0"> | |
| 2 <description> </description> | |
| 3 <command interpreter="python"> | |
| 4 experimentaldesign/experimental_design.py | |
| 5 #for $i, $f in enumerate($patients) | |
| 6 "$f.id" | |
| 7 #for $j, $g in enumerate($f.samples) | |
| 8 ${g.sample} | |
| 9 #end for | |
| 10 #end for | |
| 11 --output $out_file | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <repeat name="patients" title="Patient" min="1" default="1"> | |
| 15 <repeat name="samples" title="Sample" min="1" default="1"> | |
| 16 <param name="sample" format="tabular" type="data" label="Sample to Process" /> | |
| 17 </repeat> | |
| 18 <param name="id" type="text" label="ID" /> | |
| 19 </repeat> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data format="tabular" name="out_file" /> | |
| 23 </outputs> | |
| 24 <help> | |
| 25 Takes the ARGalaxy proprietary format and merges several samples and/or patients together. | |
| 26 </help> | |
| 27 <citations> | |
| 28 <!-- Example of annotating a citation using a DOI. --> | |
| 29 <citation type="doi">10.1093/bioinformatics/btq281</citation> | |
| 30 | |
| 31 <!-- Example of annotating a citation using a BibTex entry. --> | |
| 32 <citation type="bibtex">@ARTICLE{Kim07aninterior-point, | |
| 33 author = {Seung-jean Kim and Kwangmoo Koh and Michael Lustig and Stephen Boyd and Dimitry Gorinevsky}, | |
| 34 title = {An interior-point method for large-scale l1-regularized logistic regression}, | |
| 35 journal = {Journal of Machine Learning Research}, | |
| 36 year = {2007}, | |
| 37 volume = {8}, | |
| 38 pages = {1519-1555} | |
| 39 }</citation> | |
| 40 </citations> | |
| 41 <tests> | |
| 42 <test> | |
| 43 <param name="input" value="1.bed"/> | |
| 44 <param name="column" value="1"/> | |
| 45 <param name="order" value="ASC"/> | |
| 46 <param name="style" value="num"/> | |
| 47 <output name="out_file1" file="sort1_num.bed"/> | |
| 48 </test> | |
| 49 <test> | |
| 50 <param name="input" value="7.bed"/> | |
| 51 <param name="column" value="1"/> | |
| 52 <param name="order" value="ASC"/> | |
| 53 <param name="style" value="alpha"/> | |
| 54 <output name="out_file1" file="sort1_alpha.bed"/> | |
| 55 </test> | |
| 56 </tests> | |
| 57 </tool> |