/tools/emboss_5/emboss_merger.xml
XML | 82 lines | 78 code | 4 blank | 0 comment | 0 complexity | 1c34796174a84df7a2ca0a6db8da8741 MD5 | raw file
1<tool id="EMBOSS: merger54" name="merger" version="5.0.0"> 2 <description>Merge two overlapping nucleic acid sequences</description> 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <command>merger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto</command> 5 <inputs> 6 <param format="data" name="input1" type="data"> 7 <label>Sequence 1</label> 8 </param> 9 <param format="data" name="input2" type="data"> 10 <label>Sequence 2</label> 11 </param> 12 <param name="gapopen" size="4" type="text" value="50.0"> 13 <label>Gap opening penalty</label> 14 </param> 15 <param name="gapextend" size="4" type="text" value="5.0"> 16 <label>Gap extension penalty</label> 17 </param> 18 <param name="out_format1" 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_format2" type="select"> 51 <label>Output Alignment File Format</label> 52 <option value="simple">Simple (m)</option> 53 <option value="fasta">FASTA (m)</option> 54 <option value="msf">MSF (m)</option> 55 <option value="srs">SRS (m)</option> 56 <option value="pair">Pair (p)</option> 57 <option value="markx0">Markx0 (p)</option> 58 <option value="markx1">Markx1 (p)</option> 59 <option value="markx2">Markx2 (p)</option> 60 <option value="markx3">Markx3 (p)</option> 61 <option value="markx10">Markx10 (p)</option> 62 <option value="srspair">SRS pair (p)</option> 63 <option value="score">Score (p)</option> 64 </param> 65 </inputs> 66 <outputs> 67 <data format="fasta" name="out_file1" /> 68 <data format="simple" name="out_file2" /> 69 </outputs> 70 <code file="emboss_format_corrector.py" /> 71 <help> 72 You can view the original documentation here_. 73 74 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/merger.html 75 76------ 77 78**Citation** 79 80If 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>`_ 81 </help> 82</tool>