/tools/emboss_5/emboss_compseq.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 48 lines · 41 code · 7 blank · 0 comment · 0 complexity · 54e4b1165168dd9ba410910e6071bb2a MD5 · raw file
- <tool id="EMBOSS: compseq14" name="compseq" version="5.0.0">
- <description>Count composition of dimer/trimer/etc words in a sequence</description>
- <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
- <command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command>
- <inputs>
- <param format="fasta" name="input1" type="data">
- <label>On query</label>
- </param>
- <param name="word" size="4" type="text" value="2">
- <label>Size of word (window) to count</label>
- </param>
- <param name="frame" type="select">
- <label>Frame to inspect</label>
- <option value="0">All Frames</option>
- <option value="1">Frame 1</option>
- <option value="2">Frame 2</option>
- <option value="3">Frame 3</option>
- </param>
- </inputs>
- <outputs>
- <data format="compseq" name="out_file1" />
- </outputs>
- <tests>
- <test>
- <param name="input1" value="2.fasta"/>
- <param name="word" value="2"/>
- <param name="frame" value="0"/>
- <output name="out_file1" file="emboss_compseq_out.compseq"/>
- </test>
- </tests>
- <help>
- .. class:: warningmark
- The input dataset needs to be sequences.
- -----
- You can view the original documentation here_.
-
- .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/compseq.html
-
- ------
-
- **Citation**
-
- If 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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_
- </help>
- </tool>