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comparison emboss_trimest.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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children 8992d258e42f
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: trimest102" name="trimest" version="5.0.0.1">
2 <description>Trim poly-A tails off EST sequences</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>trimest -sequence '$input1' -outseq '$out_file1' -minlength $minlength -mismatches $mismatches -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1
9 -auto</command>
10 <inputs>
11 <param name="input1" type="data" format="fasta" label="Sequences" />
12 <param name="minlength" type="integer" value="4" label="Minimum length that a poly-A (or poly-T) tail must have before it is removed" />
13 <param name="mismatches" type="integer" value="1" label="Number of fewer mismatched non-A bases in a poly-A tail" />
14 <param name="reverse" type="select" label="Change the sequence to the forward sense when it is written out">
15 <option value="yes">Yes</option>
16 <option value="no">No</option>
17 </param>
18 <param name="tolower" type="select" label="Mask poly-A by converting to lowercase">
19 <option value="no">No</option>
20 <option value="yes">Yes</option>
21 </param>
22 <param name="fiveprime" type="select" label="Inspect 5' end of the sequence for poly-T tails">
23 <option value="yes">Yes</option>
24 <option value="no">No</option>
25 </param>
26 <param name="out_format1" type="select" label="Output sequence file format">
27 <option value="fasta">FASTA (m)</option>
28 <option value="acedb">ACeDB (m)</option>
29 <option value="asn1">ASN.1 (m)</option>
30 <option value="clustal">Clustal (m)</option>
31 <option value="codata">CODATA (m)</option>
32 <option value="embl">EMBL (m)</option>
33 <option value="fitch">Fitch (m)</option>
34 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
35 <option value="genbank">GENBANK (m)</option>
36 <option value="gff">GFF (m)</option>
37 <option value="hennig86">Hennig86 (m)</option>
38 <option value="ig">Intelligenetics (m)</option>
39 <option value="jackknifer">Jackknifer (m)</option>
40 <option value="jackknifernon">Jackknifernon (m)</option>
41 <option value="mega">Mega (m)</option>
42 <option value="meganon">Meganon (m)</option>
43 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
44 <option value="pir">NBRF (PIR) (m)</option>
45 <option value="ncbi">NCBI style FASTA (m)</option>
46 <option value="nexus">Nexus/PAUP (m)</option>
47 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
48 <option value="phylip">PHYLIP interleaved (m)</option>
49 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
50 <option value="selex">SELEX (m)</option>
51 <option value="staden">Staden (s)</option>
52 <option value="strider">DNA strider (m)</option>
53 <option value="swiss">SwisProt entry (m)</option>
54 <option value="text">Plain sequence (s)</option>
55 <option value="treecon">Treecon (m)</option>
56 </param>
57 </inputs>
58 <outputs>
59 <data name="out_file1" format="fasta" />
60 </outputs>
61 <tests>
62 <test>
63 <param name="input1" value="2.fasta"/>
64 <param name="minlength" value="4"/>
65 <param name="mismatches" value="1"/>
66 <param name="reverse" value="yes"/>
67 <param name="tolower" value="no"/>
68 <param name="fiveprime" value="yes"/>
69 <param name="out_format1" value="fasta"/>
70 <output name="out_file1" file="emboss_trimest_out.fasta"/>
71 </test>
72 </tests>
73 <help>
74 .. class:: warningmark
75
76 The input dataset needs to be sequences.
77
78 -----
79
80 You can view the original documentation here_.
81
82 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/trimest.html
83 </help>
84 <expand macro="citations" />
85 </tool>