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75 lines
3.6 KiB
XML
75 lines
3.6 KiB
XML
<tool id="EMBOSS: tranalign100" name="tranalign">
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<description>Align nucleic coding regions given the aligned proteins</description>
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<command>tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $out_format1 -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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<label>Nucleic Sequences</label>
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</param>
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<param format="data" name="input2" type="data">
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<label>Protein Sequences</label>
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</param>
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<param name="table" type="select">
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<label>Code to use</label>
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<option value="0">Standard</option>
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<option value="1">Standard (with alternative initiation codons)</option>
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<option value="2">Vertebrate Mitochondrial</option>
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<option value="3">Yeast Mitochondrial</option>
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<option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
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<option value="5">Invertebrate Mitochondrial</option>
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<option value="6">Ciliate Macronuclear and Dasycladacean</option>
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<option value="9">Echinoderm Mitochondrial</option>
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<option value="10">Euplotid Nuclear</option>
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<option value="11">Bacterial</option>
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<option value="12">Alternative Yeast Nuclear</option>
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<option value="13">Ascidian Mitochondrial</option>
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<option value="14">Flatworm Mitochondrial</option>
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<option value="15">Blepharisma Macronuclear</option>
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<option value="16">Chlorophycean Mitochondrial</option>
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<option value="21">Trematode Mitochondrial</option>
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<option value="22">Scenedesmus obliquus</option>
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<option value="23">Thraustochytrium Mitochondrial</option>
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</param>
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<param name="out_format1" type="select">
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<label>Output Sequence File Format</label>
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<option value="fasta">FASTA (m)</option>
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<option value="acedb">ACeDB (m)</option>
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<option value="asn1">ASN.1 (m)</option>
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<option value="clustal">Clustal (m)</option>
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<option value="codata">CODATA (m)</option>
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<option value="embl">EMBL (m)</option>
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<option value="fitch">Fitch (m)</option>
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<option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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<option value="genbank">GENBANK (m)</option>
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<option value="gff">GFF (m)</option>
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<option value="hennig86">Hennig86 (m)</option>
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<option value="ig">Intelligenetics (m)</option>
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<option value="jackknifer">Jackknifer (m)</option>
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<option value="jackknifernon">Jackknifernon (m)</option>
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<option value="mega">Mega (m)</option>
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<option value="meganon">Meganon (m)</option>
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<option value="msf">Wisconsin Package GCG's MSF (m)</option>
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<option value="pir">NBRF (PIR) (m)</option>
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<option value="ncbi">NCBI style FASTA (m)</option>
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<option value="nexus">Nexus/PAUP (m)</option>
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<option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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<option value="phylip">PHYLIP interleaved (m)</option>
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<option value="phylipnon">PHYLIP non-interleaved (m)</option>
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<option value="selex">SELEX (m)</option>
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<option value="staden">Staden (s)</option>
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<option value="strider">DNA strider (m)</option>
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<option value="swiss">SwisProt entry (m)</option>
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<option value="text">Plain sequence (s)</option>
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<option value="treecon">Treecon (m)</option>
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</param>
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</inputs>
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<outputs>
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<data format="fasta" name="out_file1" />
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</outputs>
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<code file="emboss_format_corrector.py" />
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<help>
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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/tranalign.html
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</help>
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</tool>
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