Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_checktrans.xml @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0"> | |
| 2 <description>Reports STOP codons and ORF statistics of a protein</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <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> | |
| 5 <inputs> | |
| 6 <param format="fasta" name="input1" type="data"> | |
| 7 <label>On query</label> | |
| 8 </param> | |
| 9 <param name="orfml" size="4" type="text" value="100"> | |
| 10 <label>Minimum ORF Length to report</label> | |
| 11 </param> | |
| 12 <param name="addlast" type="select"> | |
| 13 <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 | |
| 14 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> | |
| 15 <option value="yes">Yes</option> | |
| 16 <option value="no">No</option> | |
| 17 </param> | |
| 18 <param name="out_format2" type="select"> | |
| 19 <label>Output Sequence File Format</label> | |
| 20 <option value="fasta">FASTA (m)</option> | |
| 21 <option value="acedb">ACeDB (m)</option> | |
| 22 <option value="asn1">ASN.1 (m)</option> | |
| 23 <option value="clustal">Clustal (m)</option> | |
| 24 <option value="codata">CODATA (m)</option> | |
| 25 <option value="embl">EMBL (m)</option> | |
| 26 <option value="fitch">Fitch (m)</option> | |
| 27 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option> | |
| 28 <option value="genbank">GENBANK (m)</option> | |
| 29 <option value="gff">GFF (m)</option> | |
| 30 <option value="hennig86">Hennig86 (m)</option> | |
| 31 <option value="ig">Intelligenetics (m)</option> | |
| 32 <option value="jackknifer">Jackknifer (m)</option> | |
| 33 <option value="jackknifernon">Jackknifernon (m)</option> | |
| 34 <option value="mega">Mega (m)</option> | |
| 35 <option value="meganon">Meganon (m)</option> | |
| 36 <option value="msf">Wisconsin Package GCG's MSF (m)</option> | |
| 37 <option value="pir">NBRF (PIR) (m)</option> | |
| 38 <option value="ncbi">NCBI style FASTA (m)</option> | |
| 39 <option value="nexus">Nexus/PAUP (m)</option> | |
| 40 <option value="nexusnon">Nexusnon/PAUPnon (m)</option> | |
| 41 <option value="phylip">PHYLIP interleaved (m)</option> | |
| 42 <option value="phylipnon">PHYLIP non-interleaved (m)</option> | |
| 43 <option value="selex">SELEX (m)</option> | |
| 44 <option value="staden">Staden (s)</option> | |
| 45 <option value="strider">DNA strider (m)</option> | |
| 46 <option value="swiss">SwisProt entry (m)</option> | |
| 47 <option value="text">Plain sequence (s)</option> | |
| 48 <option value="treecon">Treecon (m)</option> | |
| 49 </param> | |
| 50 <param name="out_format3" type="select"> | |
| 51 <label>Output Feature File Format</label> | |
| 52 <option value="gff">GFF</option> | |
| 53 <option value="embl">EMBL</option> | |
| 54 <option value="swiss">SwissProt</option> | |
| 55 </param> | |
| 56 </inputs> | |
| 57 <outputs> | |
| 58 <data format="checktrans" name="out_file1" /> | |
| 59 <data format="fasta" name="out_file2" /> | |
| 60 <data format="gff" name="out_file3" /> | |
| 61 </outputs> | |
| 62 <!-- <tests> | |
| 63 <test> | |
| 64 <param name="input1" value="2.fasta"/> | |
| 65 <param name="orfml" value="100"/> | |
| 66 <param name="addlast" value="yes"/> | |
| 67 <param name="out_format2" value="fasta"/> | |
| 68 <param name="out_format3" value="gff"/> | |
| 69 <output name="out_file1" file="emboss_checktrans_out1.txt"/> | |
| 70 <output name="out_file2" file="emboss_checktrans_out2.fasta"/> | |
| 71 <output name="out_file3" file="emboss_checktrans_out3.gff"/> | |
| 72 </test> | |
| 73 </tests> --> | |
| 74 <code file="emboss_format_corrector.py" /> | |
| 75 <help> | |
| 76 | |
| 77 .. class:: warningmark | |
| 78 | |
| 79 The input dataset needs to be sequences. | |
| 80 | |
| 81 ----- | |
| 82 | |
| 83 You can view the original documentation here_. | |
| 84 | |
| 85 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/checktrans.html | |
| 86 </help> | |
| 87 </tool> |