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/tools/emboss_5/emboss_trimest.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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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
84The 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
92------
93
94**Citation**
95
96If 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;`_
97  </help>
98</tool>