Mercurial > repos > edward-kirton > lucy
comparison lucy/lucy.xml @ 0:38e2b656eb28 default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | edward-kirton |
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date | Tue, 07 Jun 2011 17:27:29 -0400 |
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1 <tool id="lucy" name="LUCY trimmer" version='1.0.1' description="Less Useful Chunks Yank"> | |
2 <command interpreter='perl'>psub -l galaxy_normal.c --fasta $fasta_infile --cat $fasta_outfile --cat $qual_outfile | |
3 lucy -quiet -xtra 8 | |
4 -error $max_avg_error $max_error_at_ends | |
5 -bracket $bracket_window_size $bracket_max_avg_error | |
6 #if $vector.vector_select == '1': | |
7 -vector $vector.vector_fasta_infile $vector.splice_fasta_infile | |
8 #end if | |
9 -output $fasta_outfile $qual_outfile | |
10 $fasta_infile $qual_infile | |
11 </command> | |
12 | |
13 <inputs> | |
14 <param name="fasta_infile" type="data" format="fasta" label="Read sequences (Fasta)"/> | |
15 <param name="qual_infile" type="data" format="qual454" label="Qual scores input file (qual454)"/> | |
16 <param name="max_avg_error" type="text" value='.007' label="max average error"/> | |
17 <param name="max_error_at_ends" type="text" value='.007' label="max error at ends"/> | |
18 <param name="bracket_window_size" type="integer" value='20' label="bracket window size"/> | |
19 <param name="bracket_max_avg_error" type="text" value='.007' label="bracket max average error"/> | |
20 | |
21 <conditional name='vector'> | |
22 <param name="vector_select" type="select" label="Do you have vector sequence files?" > | |
23 <option value="0">no, just trim by quality alone</option> | |
24 <option value="1">yes</option> | |
25 </param> | |
26 <when value='1'> | |
27 <param name="vector_fasta_infile" type="data" format="fasta" label="Complete cloning vector sequence (Fasta)"/> | |
28 <param name="splice_fasta_infile" type="data" format="fasta" label="Subsequence before and after each insert site (Fasta)"/> | |
29 </when> | |
30 <when value='0'> | |
31 </when> | |
32 </conditional> | |
33 </inputs> | |
34 <outputs> | |
35 <data name="fasta_outfile" format="fasta"/> | |
36 <data name="qual_outfile" format="qual454"/> | |
37 </outputs> | |
38 <help> | |
39 Less Useful Chunks Yank (lucy) is a utility that prepares raw DNA sequence fragments for sequence assembly. | |
40 It performs quality end-trimming and optionally removal of primer/vector sequences or filtering contamination. | |
41 | |
42 --- | |
43 | |
44 Each sequence in the output sequence file begins with a header that includes its name, three pass along | |
45 clone length values to the fragment assembly program, and a left and right marker denoting the begin and | |
46 end of the good quality, vector free region. The following is an example of lucy output:: | |
47 | |
48 >GCCAA03TF 1500 3000 2000 43 490 | |
49 AGCCAAGTTTGCAGCCCTGCAGGTCGACTCTAGAGGATCCCCAGGATGATCAGCCACATT | |
50 GGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAATGG | |
51 GCGAAAGCCTGACGCAGCCATGCCGCGTGAATGATGAAGGTCTTAGGATTGTAAAATTCT | |
52 TTCACCGGGGACGATAATGACGGTACCCGGAGAAGAAGCCCCGGCTAACTTCGTGCCAGC | |
53 ... | |
54 | |
55 --- | |
56 | |
57 **Manual** | |
58 | |
59 http://galaxy.jgi-psf.org/static/manuals/lucy.pdf | |
60 | |
61 </help> | |
62 </tool> |