Mercurial > repos > devteam > emboss_5
comparison emboss_tranalign.xml @ 12:832c20329690 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
| author | iuc |
|---|---|
| date | Mon, 23 Apr 2018 13:05:09 -0400 |
| parents | d49956b87f7e |
| children | 8992d258e42f |
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| 11:1b6538ec8b56 | 12:832c20329690 |
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| 1 <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0"> | 1 <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0"> |
| 2 <description>Align nucleic coding regions given the aligned proteins</description> | 2 <description>Align nucleic coding regions given the aligned proteins</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <code file="emboss_format_corrector.py" /> | 7 <code file="emboss_format_corrector.py" /> |
| 8 <command>tranalign -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -table $table -osformat3 $out_format1 -auto</command> | 8 <command detect_errors="aggressive"><![CDATA[ |
| 9 <inputs> | 9 tranalign |
| 10 <param name="input1" type="data" format="fasta" label="Nucleic sequences" /> | 10 -asequence '$input1' |
| 11 <param name="input2" type="data" format="data" label="Protein sequences" /> | 11 -bsequence '$input2' |
| 12 <param name="table" type="select" label="Code to use"> | 12 -outseq '$out_file1' |
| 13 <option value="0">Standard</option> | 13 -table $table |
| 14 <option value="1">Standard (with alternative initiation codons)</option> | 14 -osformat3 $out_format1 |
| 15 <option value="2">Vertebrate Mitochondrial</option> | 15 -auto |
| 16 <option value="3">Yeast Mitochondrial</option> | 16 ]]></command> |
| 17 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> | 17 <inputs> |
| 18 <option value="5">Invertebrate Mitochondrial</option> | 18 <param name="input1" argument="-asequence" type="data" format="fasta" label="Nucleic sequences" /> |
| 19 <option value="6">Ciliate Macronuclear and Dasycladacean</option> | 19 <param name="input2" argument="-bsequence" type="data" format="data" label="Protein sequences" /> |
| 20 <option value="9">Echinoderm Mitochondrial</option> | 20 <param argument="-table" type="select" label="Code to use"> |
| 21 <option value="10">Euplotid Nuclear</option> | 21 <option value="0">Standard</option> |
| 22 <option value="11">Bacterial</option> | 22 <option value="1">Standard (with alternative initiation codons)</option> |
| 23 <option value="12">Alternative Yeast Nuclear</option> | 23 <option value="2">Vertebrate Mitochondrial</option> |
| 24 <option value="13">Ascidian Mitochondrial</option> | 24 <option value="3">Yeast Mitochondrial</option> |
| 25 <option value="14">Flatworm Mitochondrial</option> | 25 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> |
| 26 <option value="15">Blepharisma Macronuclear</option> | 26 <option value="5">Invertebrate Mitochondrial</option> |
| 27 <option value="16">Chlorophycean Mitochondrial</option> | 27 <option value="6">Ciliate Macronuclear and Dasycladacean</option> |
| 28 <option value="21">Trematode Mitochondrial</option> | 28 <option value="9">Echinoderm Mitochondrial</option> |
| 29 <option value="22">Scenedesmus obliquus</option> | 29 <option value="10">Euplotid Nuclear</option> |
| 30 <option value="23">Thraustochytrium Mitochondrial</option> | 30 <option value="11">Bacterial</option> |
| 31 </param> | 31 <option value="12">Alternative Yeast Nuclear</option> |
| 32 <param name="out_format1" type="select" label="Output sequence file format"> | 32 <option value="13">Ascidian Mitochondrial</option> |
| 33 <option value="fasta">FASTA (m)</option> | 33 <option value="14">Flatworm Mitochondrial</option> |
| 34 <option value="acedb">ACeDB (m)</option> | 34 <option value="15">Blepharisma Macronuclear</option> |
| 35 <option value="asn1">ASN.1 (m)</option> | 35 <option value="16">Chlorophycean Mitochondrial</option> |
| 36 <option value="clustal">Clustal (m)</option> | 36 <option value="21">Trematode Mitochondrial</option> |
| 37 <option value="codata">CODATA (m)</option> | 37 <option value="22">Scenedesmus obliquus</option> |
| 38 <option value="embl">EMBL (m)</option> | 38 <option value="23">Thraustochytrium Mitochondrial</option> |
| 39 <option value="fitch">Fitch (m)</option> | 39 </param> |
| 40 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option> | 40 <param name="out_format1" argument="-osformat3" type="select" label="Output sequence file format"> |
| 41 <option value="genbank">GENBANK (m)</option> | 41 <option value="fasta">FASTA (m)</option> |
| 42 <option value="gff">GFF (m)</option> | 42 <option value="acedb">ACeDB (m)</option> |
| 43 <option value="hennig86">Hennig86 (m)</option> | 43 <option value="asn1">ASN.1 (m)</option> |
| 44 <option value="ig">Intelligenetics (m)</option> | 44 <option value="clustal">Clustal (m)</option> |
| 45 <option value="jackknifer">Jackknifer (m)</option> | 45 <option value="codata">CODATA (m)</option> |
| 46 <option value="jackknifernon">Jackknifernon (m)</option> | 46 <option value="embl">EMBL (m)</option> |
| 47 <option value="mega">Mega (m)</option> | 47 <option value="fitch">Fitch (m)</option> |
| 48 <option value="meganon">Meganon (m)</option> | 48 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option> |
| 49 <option value="msf">Wisconsin Package GCG's MSF (m)</option> | 49 <option value="genbank">GENBANK (m)</option> |
| 50 <option value="pir">NBRF (PIR) (m)</option> | 50 <option value="gff">GFF (m)</option> |
| 51 <option value="ncbi">NCBI style FASTA (m)</option> | 51 <option value="hennig86">Hennig86 (m)</option> |
| 52 <option value="nexus">Nexus/PAUP (m)</option> | 52 <option value="ig">Intelligenetics (m)</option> |
| 53 <option value="nexusnon">Nexusnon/PAUPnon (m)</option> | 53 <option value="jackknifer">Jackknifer (m)</option> |
| 54 <option value="phylip">PHYLIP interleaved (m)</option> | 54 <option value="jackknifernon">Jackknifernon (m)</option> |
| 55 <option value="phylipnon">PHYLIP non-interleaved (m)</option> | 55 <option value="mega">Mega (m)</option> |
| 56 <option value="selex">SELEX (m)</option> | 56 <option value="meganon">Meganon (m)</option> |
| 57 <option value="staden">Staden (s)</option> | 57 <option value="msf">Wisconsin Package GCG's MSF (m)</option> |
| 58 <option value="strider">DNA strider (m)</option> | 58 <option value="pir">NBRF (PIR) (m)</option> |
| 59 <option value="swiss">SwisProt entry (m)</option> | 59 <option value="ncbi">NCBI style FASTA (m)</option> |
| 60 <option value="text">Plain sequence (s)</option> | 60 <option value="nexus">Nexus/PAUP (m)</option> |
| 61 <option value="treecon">Treecon (m)</option> | 61 <option value="nexusnon">Nexusnon/PAUPnon (m)</option> |
| 62 </param> | 62 <option value="phylip">PHYLIP interleaved (m)</option> |
| 63 </inputs> | 63 <option value="phylipnon">PHYLIP non-interleaved (m)</option> |
| 64 <outputs> | 64 <option value="selex">SELEX (m)</option> |
| 65 <data name="out_file1" format="fasta" /> | 65 <option value="staden">Staden (s)</option> |
| 66 </outputs> | 66 <option value="strider">DNA strider (m)</option> |
| 67 <tests> | 67 <option value="swiss">SwisProt entry (m)</option> |
| 68 <test> | 68 <option value="text">Plain sequence (s)</option> |
| 69 <param name="input1" value="3.fasta"/> | 69 <option value="treecon">Treecon (m)</option> |
| 70 <param name="input2" value="2.pep"/> | 70 </param> |
| 71 <param name="table" value="0"/> | 71 </inputs> |
| 72 <param name="out_format1" value="fasta"/> | 72 <outputs> |
| 73 <output name="out_file1" file="emboss_tranalign_out.fasta"/> | 73 <data name="out_file1" format="fasta" /> |
| 74 </test> | 74 </outputs> |
| 75 </tests> | 75 <tests> |
| 76 <help> | 76 <test> |
| 77 You can view the original documentation here_. | 77 <param name="input1" value="3.fasta"/> |
| 78 <param name="input2" value="2.pep"/> | |
| 79 <param name="table" value="0"/> | |
| 80 <param name="out_format1" value="fasta"/> | |
| 81 <output name="out_file1" file="emboss_tranalign_out.fasta"/> | |
| 82 </test> | |
| 83 </tests> | |
| 84 <help><![CDATA[ | |
| 85 You can view the original documentation here_. | |
| 78 | 86 |
| 79 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html | 87 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html |
| 80 </help> | 88 ]]></help> |
| 81 <expand macro="citations" /> | 89 <expand macro="citations" /> |
| 82 </tool> | 90 </tool> |