Mercurial > repos > devteam > emboss_5
diff emboss_getorf.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
| author | iuc |
|---|---|
| date | Mon, 30 Jan 2017 13:27:40 -0500 |
| parents | 9b98d3d903c6 |
| children | 27c43fb015f0 |
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--- a/emboss_getorf.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_getorf.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,102 +1,92 @@ -<tool id="EMBOSS: getorf42" name="getorf" version="5.0.0"> - <description>Finds and extracts open reading frames (ORFs)</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>getorf -sequence $input1 -outseq $out_file1 -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking - -osformat2 $out_format1 -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="minsize" type="text" value="30"> - <label>Minimum nucleotide size of ORF to report</label> - </param> - <param name="maxsize" type="text" value="1000000"> - <label>Maximum nucleotide size of ORF to report</label> - </param> - <param name="find" type="select"> - <label>What to output</label> - <option value="0">Translation of regions between STOP codons</option> - <option value="1">Translation of regions between START and STOP codons</option> - <option value="2">Nucleic sequences between STOP codons</option> - <option value="3">Nucleic sequences between START and STOP codons</option> - <option value="4">Nucleotides flanking START codons</option> - <option value="5">Nucleotides flanking initial STOP codons</option> - <option value="6">Nucleotides flanking ending STOP codons</option> - </param> - <param name="methionine" type="select"> - <label>All START codons to code for Methionine</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="circular" type="select"> - <label>Circular sequence</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="reverse" type="select"> - <label>Find ORFs in the reverse complement</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="flanking" type="text" value="100"> - <label>Number of flanking nucleotides to output</label> - </param> - <param name="out_format1" 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="fasta" name="out_file1" /> +<tool id="EMBOSS: getorf42" name="getorf" version="5.0.0.1"> + <description>Finds and extracts open reading frames (ORFs)</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="emboss_format_corrector.py" /> + <command>getorf -sequence '$input1' -outseq '$out_file1' -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking + -osformat2 $out_format1 -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="minsize" type="integer" value="30" label="Minimum nucleotide size of ORF to report" /> + <param name="maxsize" type="integer" value="1000000" label="Maximum nucleotide size of ORF to report" /> + <param name="find" type="select" label="What to output"> + <option value="0">Translation of regions between STOP codons</option> + <option value="1">Translation of regions between START and STOP codons</option> + <option value="2">Nucleic sequences between STOP codons</option> + <option value="3">Nucleic sequences between START and STOP codons</option> + <option value="4">Nucleotides flanking START codons</option> + <option value="5">Nucleotides flanking initial STOP codons</option> + <option value="6">Nucleotides flanking ending STOP codons</option> + </param> + <param name="methionine" type="select" label="All START codons to code for Methionine"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="circular" type="select" label="Circular sequence"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="reverse" type="select" label="Find ORFs in the reverse complement"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="flanking" type="integer" value="100" label="Number of flanking nucleotides to output" /> + <param name="out_format1" 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> @@ -112,10 +102,8 @@ <param name="out_format1" value="fasta"/> <output name="out_file1" file="emboss_getorf_out.fasta"/> </test> - </tests> - <code file="emboss_format_corrector.py" /> + </tests> <help> - .. class:: warningmark The input dataset needs to be sequences. @@ -123,15 +111,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.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>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/getorf.html </help> + <expand macro="citations" /> </tool>