Mercurial > repos > devteam > emboss_5
diff emboss_transeq.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 | d5c3794bd246 |
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--- a/emboss_transeq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_transeq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,145 +1,130 @@ -<tool id="EMBOSS: transeq101" name="transeq" version="5.0.0"> - <description>Translate nucleic acid sequences</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command><![CDATA[ - transeq - -sequence '$input1' - -outseq '$out_file1' - -frame $frame - -table $table - #if str($regions).strip(): - -regions "$regions" - #end if - -trim $trim - -clean $clean - -alternative $alternative - -osformat2 '$out_format1' - -auto - ]]> - </command> - <inputs> - <param format="fasta" name="input1" type="data"> - <label>Sequences</label> - </param> - <param name="frame" type="select"> - <label>Frame(s) to translate</label> - <option value="1">Frame 1</option> - <option value="2">Frame 2</option> - <option value="3">Frame 3</option> - <option value="F">Forward three frames</option> - <option value="-1">Frame -1</option> - <option value="-2">Frame -2</option> - <option value="-3">Frame -3</option> - <option value="R">Reverse three frames</option> - <option value="6">All six frames</option> - </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="regions" type="text" value=""> - <label>Regions to translate</label> - </param> - <param name="trim" type="select"> - <label>Remove all 'X' and '*' characters from the right end of the translation</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="clean" type="select"> - <label>Change all STOP codon positions from the '*' character to 'X'</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="alternative" type="select"> - <label>Define frame '-1' as using the set of codons starting with the last codon of the sequence</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </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" /> - </outputs> - <tests> - <test> - <param name="input1" value="2.fasta"/> - <param name="frame" value="1"/> - <param name="table" value="0"/> - <param name="regions" value=""/> - <param name="trim" value="no"/> - <param name="clean" value="no"/> - <param name="alternative" value="no"/> - <param name="out_format1" value="fasta"/> - <output name="out_file1" file="emboss_transeq_out.fasta"/> - </test> - </tests> - <code file="emboss_format_corrector.py" /> - <help> - -.. class:: warningmark - -The input dataset needs to be sequences. - ------ - - You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/transeq.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>`_ - </help> -</tool> +<tool id="EMBOSS: transeq101" name="transeq" version="5.0.0"> + <description>Translate nucleic acid sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="emboss_format_corrector.py" /> + <command><![CDATA[ + transeq + -sequence '$input1' + -outseq '$out_file1' + -frame $frame + -table $table + #if str($regions).strip(): + -regions '$regions' + #end if + -trim $trim + -clean $clean + -alternative $alternative + -osformat2 '$out_format1' + -auto + ]]> + </command> + <inputs> + <param name="input1" type="data" format="fasta" label="Sequences" /> + <param name="frame" type="select" label="Frame(s) to translate"> + <option value="1">Frame 1</option> + <option value="2">Frame 2</option> + <option value="3">Frame 3</option> + <option value="F">Forward three frames</option> + <option value="-1">Frame -1</option> + <option value="-2">Frame -2</option> + <option value="-3">Frame -3</option> + <option value="R">Reverse three frames</option> + <option value="6">All six frames</option> + </param> + <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="regions" type="text" value="" label="Regions to translate" /> + <param name="trim" type="select" label="Remove all 'X' and '*' characters from the right end of the translation"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="clean" type="select" label="Change all STOP codon positions from the '*' character to 'X'"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="alternative" type="select" label="Define frame '-1' as using the set of codons starting with the last codon of the sequence"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <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> + <param name="input1" value="2.fasta"/> + <param name="frame" value="1"/> + <param name="table" value="0"/> + <param name="regions" value=""/> + <param name="trim" value="no"/> + <param name="clean" value="no"/> + <param name="alternative" value="no"/> + <param name="out_format1" value="fasta"/> + <output name="out_file1" file="emboss_transeq_out.fasta"/> + </test> + </tests> + <help> +.. class:: warningmark + +The input dataset needs to be sequences. + +----- + + You can view the original documentation here_. + + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html + </help> + <expand macro="citations" /> +</tool>