comparison tools/emboss_5/emboss_trimest.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="EMBOSS: trimest102" name="trimest" version="5.0.0">
2 <description>Trim poly-A tails off EST sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>trimest -sequence $input1 -outseq $out_file1 -minlength "$minlength" -mismatches "$mismatches" -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1
5 -auto</command>
6 <inputs>
7 <param format="fasta" name="input1" type="data">
8 <label>Sequences</label>
9 </param>
10 <param name="minlength" size="4" type="text" value="4">
11 <label>Minimum length that a poly-A (or poly-T) tail must have before it is removed</label>
12 </param>
13 <param name="mismatches" size="4" type="text" value="1">
14 <label>Number of fewer mismatched non-A bases in a poly-A tail</label>
15 </param>
16 <param name="reverse" type="select">
17 <label>Change the sequence to the forward sense when it is written out</label>
18 <option value="yes">Yes</option>
19 <option value="no">No</option>
20 </param>
21 <param name="tolower" type="select">
22 <label>Mask poly-A by converting to lowercase</label>
23 <option value="no">No</option>
24 <option value="yes">Yes</option>
25 </param>
26 <param name="fiveprime" type="select">
27 <label>Inspect 5' end of the sequence for poly-T tails</label>
28 <option value="yes">Yes</option>
29 <option value="no">No</option>
30 </param>
31 <param name="out_format1" type="select">
32 <label>Output Sequence File Format</label>
33 <option value="fasta">FASTA (m)</option>
34 <option value="acedb">ACeDB (m)</option>
35 <option value="asn1">ASN.1 (m)</option>
36 <option value="clustal">Clustal (m)</option>
37 <option value="codata">CODATA (m)</option>
38 <option value="embl">EMBL (m)</option>
39 <option value="fitch">Fitch (m)</option>
40 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
41 <option value="genbank">GENBANK (m)</option>
42 <option value="gff">GFF (m)</option>
43 <option value="hennig86">Hennig86 (m)</option>
44 <option value="ig">Intelligenetics (m)</option>
45 <option value="jackknifer">Jackknifer (m)</option>
46 <option value="jackknifernon">Jackknifernon (m)</option>
47 <option value="mega">Mega (m)</option>
48 <option value="meganon">Meganon (m)</option>
49 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
50 <option value="pir">NBRF (PIR) (m)</option>
51 <option value="ncbi">NCBI style FASTA (m)</option>
52 <option value="nexus">Nexus/PAUP (m)</option>
53 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
54 <option value="phylip">PHYLIP interleaved (m)</option>
55 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
56 <option value="selex">SELEX (m)</option>
57 <option value="staden">Staden (s)</option>
58 <option value="strider">DNA strider (m)</option>
59 <option value="swiss">SwisProt entry (m)</option>
60 <option value="text">Plain sequence (s)</option>
61 <option value="treecon">Treecon (m)</option>
62 </param>
63 </inputs>
64 <outputs>
65 <data format="fasta" name="out_file1" />
66 </outputs>
67 <tests>
68 <test>
69 <param name="input1" value="2.fasta"/>
70 <param name="minlength" value="4"/>
71 <param name="mismatches" value="1"/>
72 <param name="reverse" value="yes"/>
73 <param name="tolower" value="no"/>
74 <param name="fiveprime" value="yes"/>
75 <param name="out_format1" value="fasta"/>
76 <output name="out_file1" file="emboss_trimest_out.fasta"/>
77 </test>
78 </tests>
79 <code file="emboss_format_corrector.py" />
80 <help>
81
82 .. class:: warningmark
83
84 The input dataset needs to be sequences.
85
86 -----
87
88 You can view the original documentation here_.
89
90 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimest.html
91 </help>
92 </tool>