Mercurial > repos > devteam > emboss_5
diff emboss_sixpack.xml @ 10:9b98d3d903c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
| author | devteam |
|---|---|
| date | Fri, 12 Aug 2016 19:17:10 -0400 |
| parents | |
| children | 0e2484b6829b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/emboss_sixpack.xml Fri Aug 12 19:17:10 2016 -0400 @@ -0,0 +1,170 @@ +<tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0"> + <!-- tool adds file description and timestamp to output data --> + <description>Display a DNA sequence with 6-frame translation and ORFs</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> + <command>sixpack -sequence $input1 -outfile $ofile1 -outseq $ofile2 -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase + "$uppercase" -number $number -width "$width" -length "$length" -margin "$margin" -name $disp_name -description $description -offset "$offset" -html $html_out1 -osformat $out_format2 -auto</command> + <inputs> + <param format="fasta" name="input1" type="data"> + <label>Sequences</label> + </param> + <param name="table" type="select"> + <label>Code to use</label> + <option value="0">Standard</option> + <option value="1">Standard (with alternative initiation codons)</option> + <option value="2">Vertebrate Mitochondrial</option> + <option value="3">Yeast Mitochondrial</option> + <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> + <option value="5">Invertebrate Mitochondrial</option> + <option value="6">Ciliate Macronuclear and Dasycladacean</option> + <option value="9">Echinoderm Mitochondrial</option> + <option value="10">Euplotid Nuclear</option> + <option value="11">Bacterial</option> + <option value="12">Alternative Yeast Nuclear</option> + <option value="13">Ascidian Mitochondrial</option> + <option value="14">Flatworm Mitochondrial</option> + <option value="15">Blepharisma Macronuclear</option> + <option value="16">Chlorophycean Mitochondrial</option> + <option value="21">Trematode Mitochondrial</option> + <option value="22">Scenedesmus obliquus</option> + <option value="23">Thraustochytrium Mitochondrial</option> + </param> + <param name="firstorf" type="select"> + <label>Count the beginning of a sequence as a possible ORF</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="lastorf" type="select"> + <label>Count the end of a sequence as a possible ORF</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="mstart" type="select"> + <label>Displays only ORFs starting with an M</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="reverse" type="select"> + <label>Display the translation of the DNA sequence in the 3 reverse frames</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="orfminsize" type="text" value="1"> + <label>Minimum size of Open Reading Frames (ORFs) to display in the translations</label> + </param> + <param name="uppercase" type="text" value=""> + <label>Regions to put in uppercase</label> + </param> + <param name="number" type="select"> + <label>Number the sequence at the beginning and the end of each line</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="width" type="text" value="60"> + <label>Number of nucleotides displayed on each line</label> + </param> + <param name="length" type="text" value="0"> + <label>Line length of page</label> + </param> + <param name="margin" type="text" value="10"> + <label>Margin around sequence for numbering</label> + </param> + <param name="disp_name" type="select"> + <label>Display the ID name of the sequence</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="description" type="select"> + <label>Display the description of the sequence</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="offset" type="text" value="1"> + <label>Number from which you want the DNA sequence to be numbered</label> + </param> + <param name="html_out1" type="select"> + <label>Format output as an HTML table</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="out_format2" 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="sixpack" name="ofile1" /> + <data format="fasta" name="ofile2" /> + </outputs> +<!-- <tests> + <test> + <param name="input1" value="2.fasta"/> + <param name="table" value="0"/> + <param name="firstorf" value="no"/> + <param name="lastorf" value="no"/> + <param name="mstart" value="no"/> + <param name="reverse" value="no"/> + <param name="orfminsize" value="1"/> + <param name="uppercase" value=""/> + <param name="number" value="no"/> + <param name="width" value="60"/> + <param name="length" value="0"/> + <param name="margin" value="10"/> + <param name="disp_name" value="no"/> + <param name="description" value="no"/> + <param name="offset" value="1"/> + <param name="html_out1" value="no"/> + <param name="out_format2" value="fasta"/> + <output name="ofile2" file="emboss_sixpack_out.fasta"/> + </test> + </tests> --> + <code file="emboss_format_corrector.py" /> + <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/sixpack.html + +------ + +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + +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>