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view emboss_sixpack.xml @ 13:d5c3794bd246 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
author | iuc |
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date | Mon, 23 Apr 2018 13:04:47 -0400 |
parents | 0e2484b6829b |
children | 27c43fb015f0 |
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<tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0.1"> <!-- tool adds file description and timestamp to output data --> <description>Display a DNA sequence with 6-frame translation and ORFs</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <code file="emboss_format_corrector.py" /> <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 name="input1" type="data" format="fasta" label="Sequences" /> <param name="table" type="select" label="Code to use"> <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"> <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"> <option value="yes">Yes</option> <option value="no">No</option> </param> <param name="mstart" type="select" label="Displays only ORFs starting with an M"> <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"> <option value="yes">Yes</option> <option value="no">No</option> </param> <param name="orfminsize" type="integer" value="1" label="Minimum size of Open Reading Frames (ORFs) to display in the translations" /> <param name="uppercase" type="text" value="" label="Regions to put in uppercase" /> <param name="number" type="select" label="Number the sequence at the beginning and the end of each line"> <option value="yes">Yes</option> <option value="no">No</option> </param> <param name="width" type="integer" value="60" label="Number of nucleotides displayed on each line" /> <param name="length" type="integer" value="0" label="Line length of page" /> <param name="margin" type="integer" value="10" label="Margin around sequence for numbering" /> <param name="disp_name" type="select" label="Display the ID name of the sequence"> <option value="yes">Yes</option> <option value="no">No</option> </param> <param name="description" type="select" label="Display the description of the sequence"> <option value="yes">Yes</option> <option value="no">No</option> </param> <param name="offset" type="integer" value="1" label="Number from which you want the DNA sequence to be numbered" /> <param name="html_out1" type="select" label="Format output as an HTML table"> <option value="no">No</option> <option value="yes">Yes</option> </param> <param name="out_format2" type="select" label="Output sequence file format"> <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 name="ofile1" format="sixpack" /> <data name="ofile2" format="fasta" /> </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> --> <help> .. class:: warningmark The input dataset needs to be sequences. ----- You can view the original documentation here_. .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/sixpack.html </help> <expand macro="citations" /> </tool>