/tools/emboss_5/emboss_prettyseq.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 59 lines · 51 code · 8 blank · 0 comment · 0 complexity · ab06fc431912cdf50f0a2c4bc7a02d1d MD5 · raw file
- <tool id="EMBOSS: prettyseq80" name="prettyseq" version="5.0.0">
- <description>Output sequence with translated ranges</description>
- <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
- <command>prettyseq -sequence $input1 -outfile $out_file1 -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto</command>
- <inputs>
- <param format="fasta" name="input1" type="data">
- <label>Sequence</label>
- </param>
- <param name="ruler" type="select">
- <label>Add a ruler</label>
- <option value="yes">Yes</option>
- <option value="no">No</option>
- </param>
- <param name="plabel" type="select">
- <label>Number translations</label>
- <option value="yes">Yes</option>
- <option value="no">No</option>
- </param>
- <param name="nlabel" type="select">
- <label>Number DNA sequence</label>
- <option value="yes">Yes</option>
- <option value="no">No</option>
- </param>
- <param name="width" size="4" type="text" value="60">
- <label>Width of screen</label>
- </param>
- </inputs>
- <outputs>
- <data format="prettyseq" name="out_file1" />
- </outputs>
- <tests>
- <test>
- <param name="input1" value="2.fasta"/>
- <param name="ruler" value="yes"/>
- <param name="plabel" value="yes"/>
- <param name="nlabel" value="yes"/>
- <param name="width" value="60"/>
- <output name="out_file1" file="emboss_prettyseq_out.prettyseq"/>
- </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/prettyseq.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>