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comparison edena_ovl_wrapper.xml @ 0:60609a9cef3b draft

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author crs4
date Mon, 09 Sep 2013 05:44:31 -0400
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1 <tool id="edena_ovl_wrapper" name="Edena (overlapping)" version="0.2.2">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="3.130110">edena</requirement>
5 </requirements>
6 <version_command>edena -v</version_command>
7 <command interpreter="python">
8 edena_ovl_wrapper.py
9 \${EDENA_SITE_OPTIONS:---nThreads 2}
10 #if $input_selection.input == "unpaired_file"
11 #for $i, $unpaired_file in enumerate( $input_selection.unpaired_input ):
12 #if $i == 0
13 #echo "--unpaired_input="
14 #end if
15 #echo $unpaired_file.unpaired_file
16 #echo '+'
17 #end for
18 #elif $input_selection.input == "dr_pairs"
19 #for $i, $dr_pair_1 in enumerate( $input_selection.dr_pairs_input ):
20 #if $i == 0
21 #echo "--dr_pair_1="
22 #end if
23 #echo $dr_pair_1.dr_pair_1
24 #echo '+'
25 #end for
26 #echo ' '
27 #for $i, $dr_pair_2 in enumerate( $input_selection.dr_pairs_input ):
28 #if $i == 0
29 #echo "--dr_pair_2="
30 #end if
31 #echo $dr_pair_2.dr_pair_2
32 #echo '+'
33 #end for
34 #elif $input_selection.input == "rd_pairs"
35 #for $i, $rd_pair_1 in enumerate( $input_selection.rd_pairs_input ):
36 #if $i == 0
37 #echo "--rd_pair_1="
38 #end if
39 #echo $rd_pair_1.rd_pair_1
40 #echo '+'
41 #end for
42 #echo ' '
43 #for $i, $rd_pair_2 in enumerate( $input_selection.rd_pairs_input ):
44 #if $i == 0
45 #echo "--rd_pair_2="
46 #end if
47 #echo $rd_pair_2.rd_pair_2
48 #echo '+'
49 #end for
50 #end if
51 #if str($minOlap)
52 --minOlap=$minOlap
53 #end if
54 #if str($readsTruncation)
55 --readsTruncation=$readsTruncation
56 #end if
57 --output=$output
58 --logfile=$logfile
59 </command>
60
61 <inputs>
62 <conditional name="input_selection">
63 <param name="input" type="select" label="Select input type">
64 <option value="unpaired_file" selected="True">Unpaired files</option>
65 <option value="dr_pairs">Direct-reverse paired-end files</option>
66 <option value="rd_pairs">Reverse-direct paired-end files</option>
67 </param>
68
69 <when value="unpaired_file">
70 <repeat name="unpaired_input" title="Unpaired inputs (-r)" min="1">
71 <param name="unpaired_file" type="data" format="fasta,fastq" label="Unpaired file" help="FASTA or FASTQ format" />
72 </repeat>
73 </when>
74
75 <when value="dr_pairs">
76 <repeat name="dr_pairs_input" title="DR paired-end inputs (-DRpairs, -paired)" min="1">
77 <param name="dr_pair_1" type="data" format="fasta,fastq" label="DR paired-end file 1" help="FASTA or FASTQ format" />
78 <param name="dr_pair_2" type="data" format="fasta,fastq" label="DR paired-end file 2" help="FASTA or FASTQ format" />
79 </repeat>
80 </when>
81
82 <when value="rd_pairs">
83 <repeat name="rd_pairs_input" title="RD paired-end inputs (-RDpairs, -matePairs)" min="1">
84 <param name="rd_pair_1" type="data" format="fasta,fastq" label="RD paired-end file 1" help="FASTA or FASTQ format" />
85 <param name="rd_pair_2" type="data" format="fasta,fastq" label="RD paired-end file 2" help="FASTA or FASTQ format" />
86 </repeat>
87 </when>
88 </conditional>
89
90 <param name="minOlap" type="integer" value="" optional="true" label="Minimum overlap size to compute (-M)" help="If not specified, this value is set to half of the reads length. When the sequencing coverage is sufficient, you can increase this value which will reduce the computational time. Edena will compute the overlaps whose sizes range from this value to the reads length." />
91
92 <param name="readsTruncation" type="integer" value="" optional="true" label="3' end reads truncation (-t)" help="Use this option to truncate the 3’end of the reads such that the resulting length is the inserted value. You may consider reads truncation since it can significantly improve the assembly. Since Edena computes exact overlaps, only error free reads can take part to the assembly. Since errors are likely to occur at the 3’ ends, shortening the reads by some nucleotides may increase the number of errors-free reads in the dataset, and thus increase the assembly performance." />
93
94 </inputs>
95
96 <outputs>
97 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
98 <data name="output" format="ovl" label="${tool.name} on ${on_string}: overlapping" />
99 </outputs>
100
101 <tests>
102
103 </tests>
104 <help>
105 **What it does**
106
107 Edena can accept both unpaired and paired files, FASTQ and FASTA format. Note that for technical reasons, all reads are required to be of the same length. You can however provide the program with different files containing different reads length. In such case, Edena will trim the 3’ ends of the longer reads so that they fit the shorter length. It is however required that reads within each individual file are of the same length (as Illumina GA reads are). By default all overlaps with a minimum size corresponding to half of the reads length are computed. This is quite conservative. Provided enough coverage, this value can be increased (option -M) to reduce the memory requirements. For reads longer than 100bp, you may consider the reads truncation option, which could help in discarding 3’ base calling errors.
108
109 **License and citation**
110
111 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
112
113 .. _CRS4 Srl.: http://www.crs4.it/
114 .. _MIT license: http://opensource.org/licenses/MIT
115
116 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
117
118 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
119 .. _Cuccuru2013: http://orione.crs4.it/
120
121 This tool uses `Edena`_, which is licensed separately. Please cite |Hernandez2008|_.
122
123 .. _Edena: http://www.genomic.ch/edena.php
124 .. |Hernandez2008| replace:: Hernandez, D., *et al.* (2008) De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. *Genome Res.* 18(5), 802-809
125 .. _Hernandez2008: http://genome.cshlp.org/content/18/5/802
126 </help>
127 </tool>