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comparison emboss_trimseq.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: trimseq103" name="trimseq" version="5.0.0"> 1 <tool id="EMBOSS: trimseq103" name="trimseq" version="5.0.0.1">
2 <description>Trim ambiguous bits off the ends of sequences</description> 2 <description>Trim ambiguous bits off the ends of sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>trimseq -sequence $input1 -outseq $out_file1 -window "$window" -percent "$percent" -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>trimseq -sequence '$input1' -outseq '$out_file1' -window $window -percent $percent -strict $strict -star $star -left $left -right $right -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="Sequences" />
7 <label>Sequences</label> 11 <param name="window" type="integer" value="1" label="Window size" />
8 </param> 12 <param name="percent" type="float" value="100.0" label="Threshold of the percentage ambiguity" />
9 <param name="window" type="text" value="1"> 13 <param name="strict" type="select" label="Trim all ambiguity codes">
10 <label>Window size</label>
11 </param>
12 <param name="percent" type="text" value="100.0">
13 <label>Threshold of the percentage ambiguity</label>
14 </param>
15 <param name="strict" type="select">
16 <label>Trim all ambiguity codes</label>
17 <option value="no">No</option> 14 <option value="no">No</option>
18 <option value="yes">Yes</option> 15 <option value="yes">Yes</option>
19 </param> 16 </param>
20 <param name="star" type="select"> 17 <param name="star" type="select" label="In protein sequences, trim off not only X's, but also the *'s">
21 <label>In protein sequences, trim off not only X's, but also the *'s</label>
22 <option value="no">No</option> 18 <option value="no">No</option>
23 <option value="yes">Yes</option> 19 <option value="yes">Yes</option>
24 </param> 20 </param>
25 <param name="left" type="select"> 21 <param name="left" type="select" label="Trim at the start">
26 <label>Trim at the start</label>
27 <option value="yes">Yes</option> 22 <option value="yes">Yes</option>
28 <option value="no">No</option> 23 <option value="no">No</option>
29 </param> 24 </param>
30 <param name="right" type="select"> 25 <param name="right" type="select" label="Trim at the end">
31 <label>Trim at the end</label>
32 <option value="yes">Yes</option> 26 <option value="yes">Yes</option>
33 <option value="no">No</option> 27 <option value="no">No</option>
34 </param> 28 </param>
35 <param name="out_format1" type="select"> 29 <param name="out_format1" type="select" label="Output sequence file format">
36 <label>Output Sequence File Format</label>
37 <option value="fasta">FASTA (m)</option> 30 <option value="fasta">FASTA (m)</option>
38 <option value="acedb">ACeDB (m)</option> 31 <option value="acedb">ACeDB (m)</option>
39 <option value="asn1">ASN.1 (m)</option> 32 <option value="asn1">ASN.1 (m)</option>
40 <option value="clustal">Clustal (m)</option> 33 <option value="clustal">Clustal (m)</option>
41 <option value="codata">CODATA (m)</option> 34 <option value="codata">CODATA (m)</option>
64 <option value="text">Plain sequence (s)</option> 57 <option value="text">Plain sequence (s)</option>
65 <option value="treecon">Treecon (m)</option> 58 <option value="treecon">Treecon (m)</option>
66 </param> 59 </param>
67 </inputs> 60 </inputs>
68 <outputs> 61 <outputs>
69 <data format="fasta" name="out_file1" /> 62 <data name="out_file1" format="fasta" />
70 </outputs> 63 </outputs>
71 <tests> 64 <tests>
72 <test> 65 <test>
73 <param name="input1" value="2.fasta"/> 66 <param name="input1" value="2.fasta"/>
74 <param name="window" value="1"/> 67 <param name="window" value="1"/>
79 <param name="right" value="yes"/> 72 <param name="right" value="yes"/>
80 <param name="out_format1" value="fasta"/> 73 <param name="out_format1" value="fasta"/>
81 <output name="out_file1" file="emboss_trimseq_out.fasta"/> 74 <output name="out_file1" file="emboss_trimseq_out.fasta"/>
82 </test> 75 </test>
83 </tests> 76 </tests>
84 <code file="emboss_format_corrector.py" />
85 <help> 77 <help>
86
87 .. class:: warningmark 78 .. class:: warningmark
88 79
89 The input dataset needs to be sequences. 80 The input dataset needs to be sequences.
90 81
91 ----- 82 -----
92 83
93 You can view the original documentation here_. 84 You can view the original documentation here_.
94
95 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimseq.html
96 85
97 ------ 86 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/trimseq.html
98
99 **Citation**
100
101 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;`_
102
103 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;`_
104 </help> 87 </help>
88 <expand macro="citations" />
105 </tool> 89 </tool>