Mercurial > repos > devteam > emboss_5
view emboss_tranalign.xml @ 17:bde3097ac0f6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit d5dfff2cd58b094e0e4a6f8dc475de5facd9700b"
author | iuc |
---|---|
date | Tue, 03 Dec 2019 02:12:56 +0000 |
parents | 27c43fb015f0 |
children | 21a9fb508031 |
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<tool id="EMBOSS: tranalign100" name="tranalign" version="@VERSION@"> <description>Align nucleic coding regions given the aligned proteins</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <code file="emboss_format_corrector.py" /> <command detect_errors="aggressive"><![CDATA[ tranalign -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -table $table -osformat3 $out_format1 -auto ]]></command> <inputs> <param name="input1" argument="-asequence" type="data" format="fasta" label="Nucleic sequences" /> <param name="input2" argument="-bsequence" type="data" format="data" label="Protein sequences" /> <param argument="-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="out_format1" argument="-osformat3" 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="out_file1" format="fasta" /> </outputs> <tests> <test> <param name="input1" value="3.fasta"/> <param name="input2" value="2.pep"/> <param name="table" value="0"/> <param name="out_format1" value="fasta"/> <output name="out_file1" file="emboss_tranalign_out.fasta"/> </test> </tests> <help><![CDATA[ You can view the original documentation here_. .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html ]]></help> <expand macro="citations" /> </tool>