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comparison emboss_trimseq.xml @ 10:d49956b87f7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: trimseq103" name="trimseq" version="5.0.0.1">
2 <description>Trim ambiguous bits off the ends of sequences</description>
3 <macros>
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>
9 <inputs>
10 <param name="input1" type="data" format="fasta" label="Sequences" />
11 <param name="window" type="integer" value="1" label="Window size" />
12 <param name="percent" type="float" value="100.0" label="Threshold of the percentage ambiguity" />
13 <param name="strict" type="select" label="Trim all ambiguity codes">
14 <option value="no">No</option>
15 <option value="yes">Yes</option>
16 </param>
17 <param name="star" type="select" label="In protein sequences, trim off not only X's, but also the *'s">
18 <option value="no">No</option>
19 <option value="yes">Yes</option>
20 </param>
21 <param name="left" type="select" label="Trim at the start">
22 <option value="yes">Yes</option>
23 <option value="no">No</option>
24 </param>
25 <param name="right" type="select" label="Trim at the end">
26 <option value="yes">Yes</option>
27 <option value="no">No</option>
28 </param>
29 <param name="out_format1" type="select" label="Output sequence file format">
30 <option value="fasta">FASTA (m)</option>
31 <option value="acedb">ACeDB (m)</option>
32 <option value="asn1">ASN.1 (m)</option>
33 <option value="clustal">Clustal (m)</option>
34 <option value="codata">CODATA (m)</option>
35 <option value="embl">EMBL (m)</option>
36 <option value="fitch">Fitch (m)</option>
37 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
38 <option value="genbank">GENBANK (m)</option>
39 <option value="gff">GFF (m)</option>
40 <option value="hennig86">Hennig86 (m)</option>
41 <option value="ig">Intelligenetics (m)</option>
42 <option value="jackknifer">Jackknifer (m)</option>
43 <option value="jackknifernon">Jackknifernon (m)</option>
44 <option value="mega">Mega (m)</option>
45 <option value="meganon">Meganon (m)</option>
46 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
47 <option value="pir">NBRF (PIR) (m)</option>
48 <option value="ncbi">NCBI style FASTA (m)</option>
49 <option value="nexus">Nexus/PAUP (m)</option>
50 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
51 <option value="phylip">PHYLIP interleaved (m)</option>
52 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
53 <option value="selex">SELEX (m)</option>
54 <option value="staden">Staden (s)</option>
55 <option value="strider">DNA strider (m)</option>
56 <option value="swiss">SwisProt entry (m)</option>
57 <option value="text">Plain sequence (s)</option>
58 <option value="treecon">Treecon (m)</option>
59 </param>
60 </inputs>
61 <outputs>
62 <data name="out_file1" format="fasta" />
63 </outputs>
64 <tests>
65 <test>
66 <param name="input1" value="2.fasta"/>
67 <param name="window" value="1"/>
68 <param name="percent" value="100.0"/>
69 <param name="strict" value="no"/>
70 <param name="star" value="no"/>
71 <param name="left" value="yes"/>
72 <param name="right" value="yes"/>
73 <param name="out_format1" value="fasta"/>
74 <output name="out_file1" file="emboss_trimseq_out.fasta"/>
75 </test>
76 </tests>
77 <help>
78 .. class:: warningmark
79
80 The input dataset needs to be sequences.
81
82 -----
83
84 You can view the original documentation here_.
85
86 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/trimseq.html
87 </help>
88 <expand macro="citations" />
89 </tool>