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comparison emboss_biosed.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: biosed4" name="biosed" version="5.0.0"> 1 <tool id="EMBOSS: biosed4" name="biosed" version="5.0.0">
2 <description>Replace or delete sequence sections</description> 2 <description>Replace or delete sequence sections</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>biosed -sequence $input1 -outseq $out_file1 -target "$target" -replace "$replace" -osformat2 "$out_format1" -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>biosed -sequence '$input1' -outseq '$out_file1' -target '$target' -replace '$replace' -osformat2 $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="On query" />
7 <label>On query</label> 11 <param name="target" type="text" value="atg" label="Replace all" />
8 </param> 12 <param name="replace" type="text" value="atg" label="with" />
9 <param name="target" type="text" value="atg"> 13 <param name="out_format1" type="select" label="Output sequence file format">
10 <label>Replace all</label>
11 </param>
12 <param name="replace" type="text" value="atg">
13 <label>with</label>
14 </param>
15 <param name="out_format1" type="select">
16 <label>Output Sequence File Format</label>
17 <option value="fasta">FASTA (m)</option> 14 <option value="fasta">FASTA (m)</option>
18 <option value="acedb">ACeDB (m)</option> 15 <option value="acedb">ACeDB (m)</option>
19 <option value="asn1">ASN.1 (m)</option> 16 <option value="asn1">ASN.1 (m)</option>
20 <option value="clustal">Clustal (m)</option> 17 <option value="clustal">Clustal (m)</option>
21 <option value="codata">CODATA (m)</option> 18 <option value="codata">CODATA (m)</option>
44 <option value="text">Plain sequence (s)</option> 41 <option value="text">Plain sequence (s)</option>
45 <option value="treecon">Treecon (m)</option> 42 <option value="treecon">Treecon (m)</option>
46 </param> 43 </param>
47 </inputs> 44 </inputs>
48 <outputs> 45 <outputs>
49 <data format="txt" name="out_file1" /> 46 <data name="out_file1" format="txt" />
50 </outputs> 47 </outputs>
51 <tests> 48 <tests>
52 <test> 49 <test>
53 <param name="input1" value="2.fasta"/> 50 <param name="input1" value="2.fasta"/>
54 <param name="target" value="atg"/> 51 <param name="target" value="atg"/>
55 <param name="replace" value="agt"/> 52 <param name="replace" value="agt"/>
56 <param name="out_format1" value="fasta"/> 53 <param name="out_format1" value="fasta"/>
57 <output name="out_file1" file="emboss_biosed_out.fasta"/> 54 <output name="out_file1" file="emboss_biosed_out.fasta"/>
58 </test> 55 </test>
59 </tests> 56 </tests>
60 <code file="emboss_format_corrector.py" />
61 <help> 57 <help>
62
63 .. class:: warningmark 58 .. class:: warningmark
64 59
65 The input dataset needs to be sequences. 60 The input dataset needs to be sequences.
66 61
67 ----- 62 -----
68 63
69 You can view the original documentation here_. 64 You can view the original documentation here_.
70
71 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/biosed.html
72 65
73 ------ 66 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/biosed.html
74
75 **Citation**
76
77 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;`_
78
79 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;`_
80 </help> 67 </help>
68 <expand macro="citations" />
81 </tool> 69 </tool>