Mercurial > repos > devteam > emboss_5
diff emboss_sixpack.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_sixpack.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_sixpack.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,128 +1,108 @@ -<tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0"> +<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> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <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 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="firstorf" type="select"> - <label>Count the beginning of a sequence as a possible ORF</label> - <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</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="mstart" type="select"> - <label>Displays only ORFs starting with an M</label> - <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</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="orfminsize" type="text" value="1"> - <label>Minimum size of Open Reading Frames (ORFs) to display in the translations</label> - </param> - <param name="uppercase" type="text" value=""> - <label>Regions to put in uppercase</label> - </param> - <param name="number" type="select"> - <label>Number the sequence at the beginning and the end of each line</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="width" type="text" value="60"> - <label>Number of nucleotides displayed on each line</label> - </param> - <param name="length" type="text" value="0"> - <label>Line length of page</label> - </param> - <param name="margin" type="text" value="10"> - <label>Margin around sequence for numbering</label> - </param> - <param name="disp_name" type="select"> - <label>Display the ID name of the sequence</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="description" type="select"> - <label>Display the description of the sequence</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="offset" type="text" value="1"> - <label>Number from which you want the DNA sequence to be numbered</label> - </param> - <param name="html_out1" type="select"> - <label>Format output as an HTML table</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="out_format2" 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="sixpack" name="ofile1" /> - <data format="fasta" name="ofile2" /> + <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> @@ -145,10 +125,8 @@ <param name="out_format2" value="fasta"/> <output name="ofile2" file="emboss_sixpack_out.fasta"/> </test> - </tests> --> - <code file="emboss_format_corrector.py" /> + </tests> --> <help> - .. class:: warningmark The input dataset needs to be sequences. @@ -156,15 +134,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sixpack.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/sixpack.html </help> + <expand macro="citations" /> </tool>