/tools/emboss_5/emboss_newseq.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 78 lines · 74 code · 4 blank · 0 comment · 0 complexity · dfc536b361c3629f86c44f431d4480f5 MD5 · raw file
- <tool id="EMBOSS: newseq59" name="newseq" version="5.0.0">
- <description>Type in a short new sequence</description>
- <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
- <command>newseq -outseq $out_file1 -name "$seqname" -description "$description" -type $type -sequence "$sequence" -osformat5 $out_format1 -auto</command>
- <inputs>
- <param name="seqname" size="10" type="text" value="">
- <label>Name of of the sequence</label>
- </param>
- <param name="description" size="10" type="text" value="">
- <label>Description of the sequence</label>
- </param>
- <param name="type" type="select">
- <label>Type of sequence</label>
- <option value="N">Nucleic</option>
- <option value="P">Protein</option>
- </param>
- <param name="sequence" size="50" type="text" value="">
- <label>The sequence itself</label>
- </param>
- <param name="out_format1" type="select">
- <label>Output Sequence File Format</label>
- <option value="fasta">FASTA (m)</option>
- <option value="acedb">ACeDB (m)</option>
- <option value="asn1">ASN.1 (m)</option>
- <option value="clustal">Clustal (m)</option>
- <option value="codata">CODATA (m)</option>
- <option value="embl">EMBL (m)</option>
- <option value="fitch">Fitch (m)</option>
- <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
- <option value="genbank">GENBANK (m)</option>
- <option value="gff">GFF (m)</option>
- <option value="hennig86">Hennig86 (m)</option>
- <option value="ig">Intelligenetics (m)</option>
- <option value="jackknifer">Jackknifer (m)</option>
- <option value="jackknifernon">Jackknifernon (m)</option>
- <option value="mega">Mega (m)</option>
- <option value="meganon">Meganon (m)</option>
- <option value="msf">Wisconsin Package GCG's MSF (m)</option>
- <option value="pir">NBRF (PIR) (m)</option>
- <option value="ncbi">NCBI style FASTA (m)</option>
- <option value="nexus">Nexus/PAUP (m)</option>
- <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
- <option value="phylip">PHYLIP interleaved (m)</option>
- <option value="phylipnon">PHYLIP non-interleaved (m)</option>
- <option value="selex">SELEX (m)</option>
- <option value="staden">Staden (s)</option>
- <option value="strider">DNA strider (m)</option>
- <option value="swiss">SwisProt entry (m)</option>
- <option value="text">Plain sequence (s)</option>
- <option value="treecon">Treecon (m)</option>
- </param>
- </inputs>
- <outputs>
- <data format="fasta" name="out_file1" />
- </outputs>
- <tests>
- <test>
- <param name="seqname" value="cytoc"/>
- <param name="description" value="fragment of cytochrome c"/>
- <param name="type" value="N"/>
- <param name="sequence" value="KKKEERADLIAY"/>
- <param name="out_format1" value="fasta"/>
- <output name="out_file1" file="emboss_newseq_out.fasta"/>
- </test>
- </tests>
- <code file="emboss_format_corrector.py" />
- <help>
- You can view the original documentation here_.
-
- .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newseq.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>