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comparison emboss_maskfeat.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: maskfeat50" name="maskfeat" version="5.0.0"> 1 <tool id="EMBOSS: maskfeat50" name="maskfeat" version="5.0.0">
2 <description>Mask off features of a sequence</description> 2 <description>Mask off features of a sequence</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>maskfeat -sequence $input1 -outseq $out_file1 -type "$type" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>maskfeat -sequence '$input1' -outseq '$out_file1' -type '$type' -tolower $tolower -maskchar '$maskchar' -osformat2 $out_format1 -auto</command>
5 <inputs> 9 <inputs>
6 <param format="data" name="input1" type="data"> 10 <param name="input1" type="data" format="data" label="Sequence" />
7 <label>Sequence</label> 11 <param name="type" type="text" value="repeat*" label="Feature to mask" />
8 </param> 12 <param name="tolower" type="select" label="Mask features by converting to lowercase">
9 <param name="type" type="text" value="repeat*">
10 <label>Feature to mask</label>
11 </param>
12 <param name="tolower" type="select">
13 <label>Mask features by converting to lowercase</label>
14 <option value="no">No</option> 13 <option value="no">No</option>
15 <option value="yes">Yes</option> 14 <option value="yes">Yes</option>
16 </param> 15 </param>
17 <param name="maskchar" type="text" value="N"> 16 <param name="maskchar" type="text" value="N" label="Character to mask with" />
18 <label>Character to mask with</label> 17 <param name="out_format1" type="select" label="Output sequence file format">
19 </param>
20 <param name="out_format1" type="select">
21 <label>Output Sequence File Format</label>
22 <option value="fasta">FASTA (m)</option> 18 <option value="fasta">FASTA (m)</option>
23 <option value="acedb">ACeDB (m)</option> 19 <option value="acedb">ACeDB (m)</option>
24 <option value="asn1">ASN.1 (m)</option> 20 <option value="asn1">ASN.1 (m)</option>
25 <option value="clustal">Clustal (m)</option> 21 <option value="clustal">Clustal (m)</option>
26 <option value="codata">CODATA (m)</option> 22 <option value="codata">CODATA (m)</option>
49 <option value="text">Plain sequence (s)</option> 45 <option value="text">Plain sequence (s)</option>
50 <option value="treecon">Treecon (m)</option> 46 <option value="treecon">Treecon (m)</option>
51 </param> 47 </param>
52 </inputs> 48 </inputs>
53 <outputs> 49 <outputs>
54 <data format="fasta" name="out_file1" /> 50 <data name="out_file1" format="fasta" />
55 </outputs> 51 </outputs>
56 <tests> 52 <tests>
57 <test> 53 <test>
58 <param name="input1" value="2.fasta"/> 54 <param name="input1" value="2.fasta"/>
59 <param name="type" value="repeat*"/> 55 <param name="type" value="repeat*"/>
61 <param name="maskchar" value="N"/> 57 <param name="maskchar" value="N"/>
62 <param name="out_format1" value="fasta"/> 58 <param name="out_format1" value="fasta"/>
63 <output name="out_file1" file="emboss_maskfeat_out.fasta"/> 59 <output name="out_file1" file="emboss_maskfeat_out.fasta"/>
64 </test> 60 </test>
65 </tests> 61 </tests>
66 <code file="emboss_format_corrector.py" />
67 <help> 62 <help>
68 You can view the original documentation here_. 63 You can view the original documentation here_.
69
70 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/maskfeat.html
71 64
72 ------ 65 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/maskfeat.html
73
74 **Citation**
75
76 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;`_
77
78 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;`_
79 </help> 66 </help>
67 <expand macro="citations" />
80 </tool> 68 </tool>