Mercurial > repos > xuebing > sharplabtool
view tools/emboss_5/emboss_seqret.xml @ 1:cdcb0ce84a1b
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author | xuebing |
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date | Fri, 09 Mar 2012 19:45:15 -0500 |
parents | 9071e359b9a3 |
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<tool id="EMBOSS: seqret84" name="seqret" version="5.0.0"> <description>Reads and writes sequences</description> <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> <command>seqret -sequence $input1 -outseq $out_file1 -feature $feature -firstonly $firstonly -osformat2 $out_format1 -auto</command> <inputs> <param format="data" name="input1" type="data"> <label>Sequences</label> </param> <param name="feature" type="select"> <label>Use feature information</label> <option value="no">No</option> <option value="yes">Yes</option> </param> <param name="firstonly" type="select"> <label>Read one sequence and stop</label> <option value="no">No</option> <option value="yes">Yes</option> </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="input1" value="2.fasta"/> <param name="feature" value="no"/> <param name="firstonly" value="no"/> <param name="out_format1" value="fasta"/> <output name="out_file1" file="emboss_seqret_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/seqret.html </help> </tool>