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/tools/emboss_5/emboss_chips.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 36 lines | 32 code | 4 blank | 0 comment | 0 complexity | 0df696f048acefb8c565970fb4d08133 MD5 | raw file
 1<tool id="EMBOSS: chips10" name="chips" version="5.0.0">
 2  <description>Codon usage statistics</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>chips -seqall $input1 -outfile $out_file1 -sum $sum -auto</command>
 5  <inputs>
 6    <param format="data" name="input1" type="data">
 7      <label>On query</label>
 8    </param>
 9    <param name="sum" type="select">
10      <label>Sum codons over all sequences</label>
11      <option value="yes">Yes</option>
12      <option value="no">No</option>
13    </param>
14  </inputs>
15  <outputs>
16    <data format="chips" name="out_file1" />
17  </outputs>
18  <tests>
19    <test>
20      <param name="input1" value="2.fasta"/>
21      <param name="sum" value="yes"/>
22      <output name="out_file1" file="emboss_chips_out.chips"/>
23    </test>
24  </tests>
25  <help>
26    You can view the original documentation here_.
27    
28    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/chips.html
29
30------
31
32**Citation**
33
34If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
35  </help>
36</tool>