Mercurial > repos > devteam > emboss_5
comparison emboss_merger.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author | iuc |
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date | Mon, 30 Jan 2017 13:27:40 -0500 |
parents | 9b98d3d903c6 |
children | 27c43fb015f0 |
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10:9b98d3d903c6 | 11:0e2484b6829b |
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1 <tool id="EMBOSS: merger54" name="merger" version="5.0.0"> | 1 <tool id="EMBOSS: merger54" name="merger" version="5.0.0.1"> |
2 <description>Merge two overlapping nucleic acid sequences</description> | 2 <description>Merge two overlapping nucleic acid sequences</description> |
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | 3 <macros> |
4 <command>merger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto</command> | 4 <import>macros.xml</import> |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <code file="emboss_format_corrector.py" /> | |
8 <command>merger -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -outfile '$out_file2' -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto</command> | |
5 <inputs> | 9 <inputs> |
6 <param format="data" name="input1" type="data"> | 10 <param name="input1" type="data" format="data" label="Sequence 1" /> |
7 <label>Sequence 1</label> | 11 <param name="input2" type="data" format="data" label="Sequence 2" /> |
8 </param> | 12 <param name="gapopen" type="float" value="50.0" label="Gap opening penalty" /> |
9 <param format="data" name="input2" type="data"> | 13 <param name="gapextend" type="float" value="5.0" label="Gap extension penalty" /> |
10 <label>Sequence 2</label> | 14 <param name="out_format1" type="select" label="Output sequence file format"> |
11 </param> | |
12 <param name="gapopen" type="text" value="50.0"> | |
13 <label>Gap opening penalty</label> | |
14 </param> | |
15 <param name="gapextend" 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> | 15 <option value="fasta">FASTA (m)</option> |
21 <option value="acedb">ACeDB (m)</option> | 16 <option value="acedb">ACeDB (m)</option> |
22 <option value="asn1">ASN.1 (m)</option> | 17 <option value="asn1">ASN.1 (m)</option> |
23 <option value="clustal">Clustal (m)</option> | 18 <option value="clustal">Clustal (m)</option> |
24 <option value="codata">CODATA (m)</option> | 19 <option value="codata">CODATA (m)</option> |
45 <option value="strider">DNA strider (m)</option> | 40 <option value="strider">DNA strider (m)</option> |
46 <option value="swiss">SwisProt entry (m)</option> | 41 <option value="swiss">SwisProt entry (m)</option> |
47 <option value="text">Plain sequence (s)</option> | 42 <option value="text">Plain sequence (s)</option> |
48 <option value="treecon">Treecon (m)</option> | 43 <option value="treecon">Treecon (m)</option> |
49 </param> | 44 </param> |
50 <param name="out_format2" type="select"> | 45 <param name="out_format2" type="select" label="Output alignment file format"> |
51 <label>Output Alignment File Format</label> | |
52 <option value="simple">Simple (m)</option> | 46 <option value="simple">Simple (m)</option> |
53 <option value="fasta">FASTA (m)</option> | 47 <option value="fasta">FASTA (m)</option> |
54 <option value="msf">MSF (m)</option> | 48 <option value="msf">MSF (m)</option> |
55 <option value="srs">SRS (m)</option> | 49 <option value="srs">SRS (m)</option> |
56 <option value="pair">Pair (p)</option> | 50 <option value="pair">Pair (p)</option> |
62 <option value="srspair">SRS pair (p)</option> | 56 <option value="srspair">SRS pair (p)</option> |
63 <option value="score">Score (p)</option> | 57 <option value="score">Score (p)</option> |
64 </param> | 58 </param> |
65 </inputs> | 59 </inputs> |
66 <outputs> | 60 <outputs> |
67 <data format="fasta" name="out_file1" /> | 61 <data name="out_file1" format="fasta" /> |
68 <data format="simple" name="out_file2" /> | 62 <data name="out_file2" format="simple" /> |
69 </outputs> | 63 </outputs> |
70 <code file="emboss_format_corrector.py" /> | |
71 <help> | 64 <help> |
72 You can view the original documentation here_. | 65 You can view the original documentation here_. |
73 | |
74 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/merger.html | |
75 | 66 |
76 ------ | 67 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/merger.html |
77 | |
78 **Citation** | |
79 | |
80 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>`_ | |
81 | |
82 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>`_ | |
83 </help> | 68 </help> |
69 <expand macro="citations" /> | |
84 </tool> | 70 </tool> |