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comparison emboss_extractfeat.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: extractfeat34" name="extractfeat" version="5.0.0"> 1 <tool id="EMBOSS: extractfeat34" name="extractfeat" version="5.0.0.1">
2 <!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences --> 2 <!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences -->
3 <description>Extract features from a sequence</description> 3 <description>Extract features from a sequence</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <macros>
5 <command>extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value 5 <import>macros.xml</import>
6 "$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto</command> 6 </macros>
7 <expand macro="requirements" />
8 <code file="emboss_format_corrector.py" />
9 <command>extractfeat -sequence '$input1' -outseq '$out_file1' -before $before -after $after -source '$source' -type '$type' -sense $sense -minscore $minscore -maxscore $maxscore -tag '$tag' -value
10 '$value' -join $join -featinname $featinname -describe '$describe' -osformat2 $out_format1 -auto</command>
7 <inputs> 11 <inputs>
8 <param format="data" name="input1" type="data"> 12 <param name="input1" type="data" format="data" label="Sequences" />
9 <label>Sequences</label> 13 <param name="before" type="integer" value="0" label="Number of bases or residues before the feature to include in the extracted sequence" />
10 </param> 14 <param name="after" type="integer" value="0" label="Number of bases or residues after the feature to include in the extracted sequence" />
11 <param name="before" type="text" value="0"> 15 <param name="source" type="text" value="*" label="Feature source" />
12 <label>Number of bases or residues before the feature to include in the extracted sequence</label> 16 <param name="type" type="text" value="*" label="Feature type" />
13 </param> 17 <param name="sense" type="select" label="Feature sense">
14 <param name="after" type="text" value="0">
15 <label>Number of bases or residues after the feature to include in the extracted sequence</label>
16 </param>
17 <param name="source" type="text" value="*">
18 <label>Feature source</label>
19 </param>
20 <param name="type" type="text" value="*">
21 <label>Feature type</label>
22 </param>
23 <param name="sense" type="select">
24 <label>Feature sense</label>
25 <option value="0">Any sense</option> 18 <option value="0">Any sense</option>
26 <option value="1">Forward sense</option> 19 <option value="1">Forward sense</option>
27 <option value="-1">Reverse sense</option> 20 <option value="-1">Reverse sense</option>
28 </param> 21 </param>
29 <param name="minscore" type="text" value="0.0"> 22 <param name="minscore" type="float" value="0.0" label="Minimum score" />
30 <label>Minimum score</label> 23 <param name="maxscore" type="float" value="0.0" label="Maximum score" />
31 </param> 24 <param name="tag" type="text" value="*" label="Feature tags" />
32 <param name="maxscore" type="text" value="0.0"> 25 <param name="value" type="text" value="*" label="Tag values" />
33 <label>Maximum score</label> 26 <param name="join" type="select" label="Join features">
34 </param>
35 <param name="tag" type="text" value="*">
36 <label>Feature tags</label>
37 </param>
38 <param name="value" type="text" value="*">
39 <label>Tag values</label>
40 </param>
41 <param name="join" type="select">
42 <label>Join features</label>
43 <option value="no">No</option> 27 <option value="no">No</option>
44 <option value="yes">Yes</option> 28 <option value="yes">Yes</option>
45 </param> 29 </param>
46 <param name="featinname" type="select"> 30 <param name="featinname" type="select" label="Put feature type in sequence name">
47 <label>Put feature type in sequence name</label>
48 <option value="no">No</option> 31 <option value="no">No</option>
49 <option value="yes">Yes</option> 32 <option value="yes">Yes</option>
50 </param> 33 </param>
51 <param name="describe" type="text" value=""> 34 <param name="describe" type="text" value="" label="Specify one or more tag names that should be added to the output sequence Description text" />
52 <label>Specify one or more tag names that should be added to the output sequence Description text</label> 35 <param name="out_format1" type="select" label="Output sequence file format">
53 </param>
54 <param name="out_format1" type="select">
55 <label>Output Sequence File Format</label>
56 <option value="fasta">FASTA (m)</option> 36 <option value="fasta">FASTA (m)</option>
57 <option value="acedb">ACeDB (m)</option> 37 <option value="acedb">ACeDB (m)</option>
58 <option value="asn1">ASN.1 (m)</option> 38 <option value="asn1">ASN.1 (m)</option>
59 <option value="clustal">Clustal (m)</option> 39 <option value="clustal">Clustal (m)</option>
60 <option value="codata">CODATA (m)</option> 40 <option value="codata">CODATA (m)</option>
83 <option value="text">Plain sequence (s)</option> 63 <option value="text">Plain sequence (s)</option>
84 <option value="treecon">Treecon (m)</option> 64 <option value="treecon">Treecon (m)</option>
85 </param> 65 </param>
86 </inputs> 66 </inputs>
87 <outputs> 67 <outputs>
88 <data format="fasta" name="out_file1" /> 68 <data name="out_file1" format="fasta" />
89 </outputs> 69 </outputs>
90 <code file="emboss_format_corrector.py" />
91 <help> 70 <help>
92 You can view the original documentation here_. 71 You can view the original documentation here_.
93
94 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractfeat.html
95 72
96 ------ 73 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/extractfeat.html
97
98 **Citation**
99
100 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;`_
101
102 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;`_
103 </help> 74 </help>
75 <expand macro="citations" />
104 </tool> 76 </tool>