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comparison emboss_msbar.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: msbar55" name="msbar" version="5.0.0"> 1 <tool id="EMBOSS: msbar55" name="msbar" version="5.0.0.1">
2 <description>Mutate sequence beyond all recognition</description> 2 <description>Mutate sequence beyond all recognition</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>msbar -sequence $input1 -outseq $out_file1 -count $count -point $point -block $block -codon $codon -inframe $inframe -minimum $minimum -maximum $maximum -osformat2 $out_format1 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>msbar -sequence '$input1' -outseq '$out_file1' -count $count -point $point -block $block -codon $codon -inframe $inframe -minimum $minimum -maximum $maximum -osformat2 $out_format1
5 -auto</command> 9 -auto</command>
6 <inputs> 10 <inputs>
7 <param format="fasta" name="input1" type="data"> 11 <param name="input1" type="data" format="fasta" label="Sequence 1" />
8 <label>Sequence 1</label> 12 <param name="count" type="integer" value="1" label="Number of times to perform the mutation operations" />
9 </param> 13 <param name="point" type="select" label="Types of point mutations to perform">
10 <param name="count" type="text" value="1">
11 <label>Number of times to perform the mutation operations</label>
12 </param>
13 <param name="point" type="select">
14 <label>Types of point mutations to perform</label>
15 <option value="0">None</option> 14 <option value="0">None</option>
16 <option value="1">Any of the following</option> 15 <option value="1">Any of the following</option>
17 <option value="2">Insertions</option> 16 <option value="2">Insertions</option>
18 <option value="3">Deletions</option> 17 <option value="3">Deletions</option>
19 <option value="4">Changes</option> 18 <option value="4">Changes</option>
20 <option value="5">Duplications</option> 19 <option value="5">Duplications</option>
21 <option value="6">Moves</option> 20 <option value="6">Moves</option>
22 </param> 21 </param>
23 <param name="block" type="select"> 22 <param name="block" type="select" label="Types of block mutations to perform">
24 <label>Types of block mutations to perform</label>
25 <option value="0">None</option> 23 <option value="0">None</option>
26 <option value="1">Any of the following</option> 24 <option value="1">Any of the following</option>
27 <option value="2">Insertions</option> 25 <option value="2">Insertions</option>
28 <option value="3">Deletions</option> 26 <option value="3">Deletions</option>
29 <option value="4">Changes</option> 27 <option value="4">Changes</option>
30 <option value="5">Duplications</option> 28 <option value="5">Duplications</option>
31 <option value="6">Moves</option> 29 <option value="6">Moves</option>
32 </param> 30 </param>
33 <param name="codon" type="select"> 31 <param name="codon" type="select" label="Types of codon mutations to perform" help="These are only done if the sequence is nucleic">
34 <label>Types of codon mutations to perform. These are only done if the sequence is nucleic</label>
35 <option value="0">None</option> 32 <option value="0">None</option>
36 <option value="1">Any of the following</option> 33 <option value="1">Any of the following</option>
37 <option value="2">Insertions</option> 34 <option value="2">Insertions</option>
38 <option value="3">Deletions</option> 35 <option value="3">Deletions</option>
39 <option value="4">Changes</option> 36 <option value="4">Changes</option>
40 <option value="5">Duplications</option> 37 <option value="5">Duplications</option>
41 <option value="6">Moves</option> 38 <option value="6">Moves</option>
42 </param> 39 </param>
43 <param name="inframe" type="select"> 40 <param name="inframe" type="select" label="Do 'codon' and 'block' operations in frame">
44 <label>Do 'codon' and 'block' operations in frame</label>
45 <option value="no">No</option> 41 <option value="no">No</option>
46 <option value="yes">Yes</option> 42 <option value="yes">Yes</option>
47 </param> 43 </param>
48 <param name="minimum" type="text" value="1"> 44 <param name="minimum" type="integer" value="1" label="Minimum size for a block mutation" />
49 <label>Minimum size for a block mutation</label> 45 <param name="maximum" type="integer" value="10" label="Maximum size for a block mutation" />
50 </param> 46 <param name="out_format1" type="select" label="Output sequence file format">
51 <param name="maximum" type="text" value="10">
52 <label>Maximum size for a block mutation</label>
53 </param>
54 <param name="out_format1" type="select">
55 <label>Output Sequence File Format</label>
56 <option value="fasta">FASTA (m)</option> 47 <option value="fasta">FASTA (m)</option>
57 <option value="acedb">ACeDB (m)</option> 48 <option value="acedb">ACeDB (m)</option>
58 <option value="asn1">ASN.1 (m)</option> 49 <option value="asn1">ASN.1 (m)</option>
59 <option value="clustal">Clustal (m)</option> 50 <option value="clustal">Clustal (m)</option>
60 <option value="codata">CODATA (m)</option> 51 <option value="codata">CODATA (m)</option>
83 <option value="text">Plain sequence (s)</option> 74 <option value="text">Plain sequence (s)</option>
84 <option value="treecon">Treecon (m)</option> 75 <option value="treecon">Treecon (m)</option>
85 </param> 76 </param>
86 </inputs> 77 </inputs>
87 <outputs> 78 <outputs>
88 <data format="fasta" name="out_file1" /> 79 <data name="out_file1" format="fasta" />
89 </outputs> 80 </outputs>
90 <tests> 81 <tests>
91 <test> 82 <test>
92 <param name="input1" value="2.fasta"/> 83 <param name="input1" value="2.fasta"/>
93 <param name="count" value="1"/> 84 <param name="count" value="1"/>
99 <param name="maximum" value="10"/> 90 <param name="maximum" value="10"/>
100 <param name="out_format1" value="fasta"/> 91 <param name="out_format1" value="fasta"/>
101 <output name="out_file1" file="emboss_msbar_out.fasta"/> 92 <output name="out_file1" file="emboss_msbar_out.fasta"/>
102 </test> 93 </test>
103 </tests> 94 </tests>
104 <code file="emboss_format_corrector.py" />
105 <help> 95 <help>
106
107 .. class:: warningmark 96 .. class:: warningmark
108 97
109 The input dataset needs to be sequences. 98 The input dataset needs to be sequences.
110 99
111 ----- 100 -----
112 101
113 You can view the original documentation here_. 102 You can view the original documentation here_.
114
115 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/msbar.html
116 103
117 ------ 104 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/msbar.html
118
119 **Citation**
120
121 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;`_
122
123 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;`_
124 </help> 105 </help>
106 <expand macro="citations" />
125 </tool> 107 </tool>