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comparison emboss_sirna.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: sirna89" name="sirna" version="5.0.0"> 1 <tool id="EMBOSS: sirna89" name="sirna" version="5.0.0">
2 <description>Finds siRNA duplexes in mRNA</description> 2 <description>Finds siRNA duplexes in mRNA</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>sirna -sequence $input1 -outfile $ofile1 -outseq $ofile2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>sirna -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2
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="Sequences" />
8 <label>Sequences</label> 12 <param name="poliii" type="select" label="Select only the 21 base probes that start with a purine (Pol III expression vectors)">
9 </param>
10 <param name="poliii" type="select">
11 <label>Select only the 21 base probes that start with a purine (Pol III expression vectors)</label>
12 <option value="no">No</option> 13 <option value="no">No</option>
13 <option value="yes">Yes</option> 14 <option value="yes">Yes</option>
14 </param> 15 </param>
15 <param name="aa" type="select"> 16 <param name="aa" type="select" label="Select only those 23 base regions that start with AA">
16 <label>Select only those 23 base regions that start with AA</label>
17 <option value="no">No</option> 17 <option value="no">No</option>
18 <option value="yes">Yes</option> 18 <option value="yes">Yes</option>
19 </param> 19 </param>
20 <param name="tt" type="select"> 20 <param name="tt" type="select" label="Select only those 23 base regions that end with TT">
21 <label>Select only those 23 base regions that end with TT</label>
22 <option value="no">No</option> 21 <option value="no">No</option>
23 <option value="yes">Yes</option> 22 <option value="yes">Yes</option>
24 </param> 23 </param>
25 <param name="polybase" type="select"> 24 <param name="polybase" type="select" label="Report more than those 23 base regions that have no repeat of 4 or more of any bases in a row">
26 <label>Report more than those 23 base regions that have no repeat of 4 or more of any bases in a row</label>
27 <option value="yes">Yes</option> 25 <option value="yes">Yes</option>
28 <option value="no">No</option> 26 <option value="no">No</option>
29 </param> 27 </param>
30 <param name="context" type="select"> 28 <param name="context" type="select" label="Displays the whole 23 bases of the region with the first two bases in brackets">
31 <label>Displays the whole 23 bases of the region with the first two bases in brackets</label>
32 <option value="no">No</option> 29 <option value="no">No</option>
33 <option value="yes">Yes</option> 30 <option value="yes">Yes</option>
34 </param> 31 </param>
35 <param name="out_format1" type="select"> 32 <param name="out_format1" type="select" label="Output report file format">
36 <label>Output Report File Format</label>
37 <option value="table">Table</option> 33 <option value="table">Table</option>
38 <option value="embl">EMBL</option> 34 <option value="embl">EMBL</option>
39 <option value="genbank">GENBANK</option> 35 <option value="genbank">GENBANK</option>
40 <option value="gff">GFF</option> 36 <option value="gff">GFF</option>
41 <option value="pir">PIR</option> 37 <option value="pir">PIR</option>
49 <option value="seqtable">SeqTable</option> 45 <option value="seqtable">SeqTable</option>
50 <option value="simple">SRS Simple</option> 46 <option value="simple">SRS Simple</option>
51 <option value="srs">SRS</option> 47 <option value="srs">SRS</option>
52 <option value="tagseq">TagSeq</option> 48 <option value="tagseq">TagSeq</option>
53 </param> 49 </param>
54 <param name="out_format2" type="select"> 50 <param name="out_format2" type="select" label="Output sequence file format">
55 <label>Output Sequence File Format</label>
56 <option value="fasta">FASTA (m)</option> 51 <option value="fasta">FASTA (m)</option>
57 <option value="acedb">ACeDB (m)</option> 52 <option value="acedb">ACeDB (m)</option>
58 <option value="asn1">ASN.1 (m)</option> 53 <option value="asn1">ASN.1 (m)</option>
59 <option value="clustal">Clustal (m)</option> 54 <option value="clustal">Clustal (m)</option>
60 <option value="codata">CODATA (m)</option> 55 <option value="codata">CODATA (m)</option>
83 <option value="text">Plain sequence (s)</option> 78 <option value="text">Plain sequence (s)</option>
84 <option value="treecon">Treecon (m)</option> 79 <option value="treecon">Treecon (m)</option>
85 </param> 80 </param>
86 </inputs> 81 </inputs>
87 <outputs> 82 <outputs>
88 <data format="table" name="ofile1" /> 83 <data name="ofile1" format="table" />
89 <data format="fasta" name="ofile2" /> 84 <data name="ofile2" format="fasta" />
90 </outputs> 85 </outputs>
91 <tests> 86 <tests>
92 <test> 87 <test>
93 <param name="input1" value="2.fasta"/> 88 <param name="input1" value="2.fasta"/>
94 <param name="poliii" value="no"/> 89 <param name="poliii" value="no"/>
100 <param name="out_format1" value="gff"/> 95 <param name="out_format1" value="gff"/>
101 <param name="out_format2" value="fasta"/> 96 <param name="out_format2" value="fasta"/>
102 <output name="ofile2" file="emboss_sirna_out.fasta"/> 97 <output name="ofile2" file="emboss_sirna_out.fasta"/>
103 </test> 98 </test>
104 </tests> 99 </tests>
105 <code file="emboss_format_corrector.py" />
106 <help> 100 <help>
107
108 .. class:: warningmark 101 .. class:: warningmark
109 102
110 The input dataset needs to be sequences. 103 The input dataset needs to be sequences.
111 104
112 ----- 105 -----
113 106
114 You can view the original documentation here_. 107 You can view the original documentation here_.
115
116 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sirna.html
117 108
118 ------ 109 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/sirna.html
119
120 **Citation**
121
122 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;`_
123
124 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;`_
125 </help> 110 </help>
111 <expand macro="citations" />
126 </tool> 112 </tool>