Mercurial > repos > devteam > emboss_5
diff emboss_checktrans.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 |
line wrap: on
line diff
--- a/emboss_checktrans.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_checktrans.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,63 +1,59 @@ -<tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0"> - <description>Reports STOP codons and ORF statistics of a protein</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>checktrans -sequence $input1 -outfile $out_file1 -outseq $out_file2 -osformat3 $out_format2 -outfeat $out_file3 -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto</command> - <inputs> - <param format="fasta" name="input1" type="data"> - <label>On query</label> - </param> - <param name="orfml" type="text" value="100"> - <label>Minimum ORF Length to report</label> - </param> - <param name="addlast" type="select"> - <label>An asterisk in the protein sequence indicates the position of a STOP codon. Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there - is not one there already, makes checktrans treat the end as a potential ORF. If an asterisk is added, it is not included in the reported count of STOPs</label> - <option value="yes">Yes</option> - <option value="no">No</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> - <param name="out_format3" type="select"> - <label>Output Feature File Format</label> - <option value="gff">GFF</option> - <option value="embl">EMBL</option> - <option value="swiss">SwissProt</option> - </param> - </inputs> - <outputs> - <data format="checktrans" name="out_file1" /> - <data format="fasta" name="out_file2" /> - <data format="gff" name="out_file3" /> +<tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0.1"> + <description>Reports STOP codons and ORF statistics of a protein</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="emboss_format_corrector.py" /> + <command>checktrans -sequence '$input1' -outfile '$out_file1' -outseq '$out_file2' -osformat3 $out_format2 -outfeat '$out_file3' -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto</command> + <inputs> + <param name="input1" type="data" format="fasta" label="On query" /> + <param name="orfml" type="integer" value="100" label="Minimum ORF length to report" /> + <param name="addlast" type="select" label="An asterisk in the protein sequence indicates the position of a STOP codon" help="Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there is not one there already, makes checktrans treat the end as a potential ORF. If an asterisk is added, it is not included in the reported count of STOPs"> + <option value="yes">Yes</option> + <option value="no">No</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> + <param name="out_format3" type="select" label="Output feature file format"> + <option value="gff">GFF</option> + <option value="embl">EMBL</option> + <option value="swiss">SwissProt</option> + </param> + </inputs> + <outputs> + <data name="out_file1" format="checktrans" /> + <data name="out_file2" format="fasta" /> + <data name="out_file3" format="gff" /> </outputs> <!-- <tests> <test> @@ -70,26 +66,17 @@ <output name="out_file2" file="emboss_checktrans_out2.fasta"/> <output name="out_file3" file="emboss_checktrans_out3.gff"/> </test> - </tests> --> - <code file="emboss_format_corrector.py" /> + </tests> --> <help> +.. class:: warningmark -.. class:: warningmark +The input dataset needs to be sequences. -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/checktrans.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/checktrans.html </help> + <expand macro="citations" /> </tool>