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comparison emboss_fuzztran.xml @ 11:0e2484b6829b draft

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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
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10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0"> 1 <tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0.1">
2 <description>Protein pattern search after translation</description> 2 <description>Protein pattern search after translation</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>fuzztran -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
5 <inputs> 9 <inputs>
6 <param format="fasta" name="input1" type="data"> 10 <param name="input1" type="data" format="fasta" label="Sequences" />
7 <label>Sequences</label> 11 <param name="pattern" type="text" value="" label="Search pattern" />
8 </param> 12 <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
9 <param name="pattern" type="text" value=""> 13 <param name="frame" type="select" label="Frame(s) to translate">
10 <label>Search pattern</label>
11 </param>
12 <param name="mismatch" type="text" value="0">
13 <label>Number of mismatches</label>
14 </param>
15 <param name="frame" type="select">
16 <label>Frame(s) to translate</label>
17 <option value="1">Frame 1</option> 14 <option value="1">Frame 1</option>
18 <option value="2">Frame 2</option> 15 <option value="2">Frame 2</option>
19 <option value="3">Frame 3</option> 16 <option value="3">Frame 3</option>
20 <option value="F">Forward three frames</option> 17 <option value="F">Forward three frames</option>
21 <option value="-1">Frame -1</option> 18 <option value="-1">Frame -1</option>
22 <option value="-2">Frame -2</option> 19 <option value="-2">Frame -2</option>
23 <option value="-3">Frame -3</option> 20 <option value="-3">Frame -3</option>
24 <option value="R">Reverse three frames</option> 21 <option value="R">Reverse three frames</option>
25 <option value="6">All six frames</option> 22 <option value="6">All six frames</option>
26 </param> 23 </param>
27 <param name="table" type="select"> 24 <param name="table" type="select" label="Code to use">
28 <label>Code to use</label>
29 <option value="0">Standard</option> 25 <option value="0">Standard</option>
30 <option value="1">Standard (with alternative initiation codons)</option> 26 <option value="1">Standard (with alternative initiation codons)</option>
31 <option value="2">Vertebrate Mitochondrial</option> 27 <option value="2">Vertebrate Mitochondrial</option>
32 <option value="3">Yeast Mitochondrial</option> 28 <option value="3">Yeast Mitochondrial</option>
33 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> 29 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
43 <option value="16">Chlorophycean Mitochondrial</option> 39 <option value="16">Chlorophycean Mitochondrial</option>
44 <option value="21">Trematode Mitochondrial</option> 40 <option value="21">Trematode Mitochondrial</option>
45 <option value="22">Scenedesmus obliquus</option> 41 <option value="22">Scenedesmus obliquus</option>
46 <option value="23">Thraustochytrium Mitochondrial</option> 42 <option value="23">Thraustochytrium Mitochondrial</option>
47 </param> 43 </param>
48 <param name="out_format1" type="select"> 44 <param name="out_format1" type="select" label="Output report file format">
49 <label>Output Report File Format</label>
50 <option value="table">Table</option> 45 <option value="table">Table</option>
51 <option value="embl">EMBL</option> 46 <option value="embl">EMBL</option>
52 <option value="genbank">GENBANK</option> 47 <option value="genbank">GENBANK</option>
53 <option value="gff">GFF</option> 48 <option value="gff">GFF</option>
54 <option value="pir">PIR</option> 49 <option value="pir">PIR</option>
64 <option value="srs">SRS</option> 59 <option value="srs">SRS</option>
65 <option value="tagseq">TagSeq</option> 60 <option value="tagseq">TagSeq</option>
66 </param> 61 </param>
67 </inputs> 62 </inputs>
68 <outputs> 63 <outputs>
69 <data format="fuzztran" name="out_file1" /> 64 <data name="out_file1" format="fuzztran" />
70 </outputs> 65 </outputs>
71 <tests> 66 <tests>
72 <test> 67 <test>
73 <param name="input1" value="1.fasta"/> 68 <param name="input1" value="1.fasta"/>
74 <param name="pattern" value="AA"/> 69 <param name="pattern" value="AA"/>
77 <param name="table" value="0"/> 72 <param name="table" value="0"/>
78 <param name="out_format1" value="excel"/> 73 <param name="out_format1" value="excel"/>
79 <output name="out_file1" file="emboss_fuzztran_out.tabular"/> 74 <output name="out_file1" file="emboss_fuzztran_out.tabular"/>
80 </test> 75 </test>
81 </tests> 76 </tests>
82 <code file="emboss_format_corrector.py" />
83 <help> 77 <help>
84
85 .. class:: warningmark 78 .. class:: warningmark
86 79
87 The input dataset needs to be sequences. 80 The input dataset needs to be sequences.
88 81
89 ----- 82 -----
90 83
91 You can view the original documentation here_. 84 You can view the original documentation here_.
92
93 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzztran.html
94 85
95 ------ 86 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzztran.html
96
97 **Citation**
98
99 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
100
101 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
102 </help> 87 </help>
88 <expand macro="citations" />
103 </tool> 89 </tool>