Mercurial > repos > crs4 > glimmer

comparison glimmer3_wrapper.xml @ 0:9c8ffce71f7c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author crs4
date Mon, 09 Sep 2013 12:16:17 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9c8ffce71f7c
1 <tool id="glimmer3_wrapper" name="Glimmer3" version="0.2">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="3.02">glimmer</requirement>
5 </requirements>
6 <command interpreter="python">
7 glimmer3_wrapper.py --glSequence $glSequence --glIcm $glIcm
8 #if $glStartCodons
9 --glStartCodons="$glStartCodons"
10 #end if
11 #if $glRbsPwm
12 --glRbsPwm=$glRbsPwm
13 #end if
14 #if str($glGcPercent)
15 --glGcPercent=$glGcPercent
16 #end if
17 #if $glEntropy.glEntropy_select == 'default'
18 --glEntropy='#'
19 #else if $glEntropy.glEntropy_select == 'fromfile'
20 --glEntropy=${glEntropy.glEntropyFile}
21 #end if
22 #if $glFirstCodon
23 --glFirstCodon
24 #end if
25 #if str($glGeneLen)
26 --glGeneLen=$glGeneLen
27 #end if
28 #if $glLinear
29 --glLinear
30 #end if
31 #if $glOrfCoords
32 --glOrfCoords=$glOrfCoords
33 #end if
34 #if $glSeparateGenes
35 --glSeparateGenes
36 #end if
37 #if str($glMaxOverlap)
38 --glMaxOverlap=$glMaxOverlap
39 #end if
40 #if $glStartProbs
41 --glStartProbs="$glStartProbs"
42 #end if
43 #if str($glIgnoreScoreLen)
44 --glIgnoreScoreLen=$glIgnoreScoreLen
45 #end if
46 #if $glNoIndep
47 --glNoIndep
48 #end if
49 #if str($glThreshold)
50 --glThreshold=$glThreshold
51 #end if
52 #if $glExtend
53 --glExtend
54 #end if
55 #if str($glTransTable)
56 --glTransTable=$glTransTable
57 #end if
58 #if $glStopCodons
59 --glStopCodons="$glStopCodons"
60 #end if
61 --glDetail $glDetail --glPredict $glPredict --logfile $logfile
62 </command>
63
64 <inputs>
65 <param name="glSequence" type="data" format="fasta" label="DNA sequences to be analyzed" help="FASTA format" />
66
67 <param name="glIcm" type="data" format="glimmer_icm" label="ICM model produced by Build-ICM" />
68
69 <param name="glStartCodons" type="text" value="" optional="true" label="Specify allowable start codons as a comma-separated list (-A, --start_codons)" help="Sample format: 'atg,gtg' . The default start codons are atg, gtg and ttg. Use the 'GC percentage' option to specify the relative proportions of use, elsethe the proportions will be equal." />
70
71 <param name="glRbsPwm" type="data" format="glimmer_pwm" optional="true" label="Position weight matrix representing the ribosome binding site for genes (-b, --rbs_pwm)" help="Used to improve the accuracy of start site predictions." />
72
73 <param name="glGcPercent" type="float" value="" optional="true" label="GC percentage of the independent model, e.g. 45.2 (-C, --gc_percent)" help="If this option is not specified, the GC percentage will be counted from the input file." />
74
75 <conditional name="glEntropy">
76 <param name="glEntropy_select" type="select" label="Use entropy profiles (-E, --entropy)">
77 <option value="no">No</option>
78 <option value="default">Use default entropy profiles, constructed from a wide range of species (-E #)</option>
79 <option value="fromfile">Use entropy profiles from history</option>
80 </param>
81 <when value="no" />
82 <when value="default" />
83 <when value="fromfile">
84 <param name="glEntropyFile" type="data" format="glimmer_entropy_profiles" label="Entropy profiles" help="As generated by Glimmer entropy-profile" />
85 </when>
86 </conditional>
87
88 <param name="glFirstCodon" type="boolean" checked="false" label="Use the first possible codon in an ORF as the start codon for initial scoring purposes (-f, --first_codon)" help="Otherwise, the highest-scoring codon will be used. This only affects the start positions in the .detail file. The final start predictions in the .predict file are always based on the scoring functions." />
89
90 <param name="glGeneLen" type="integer" value="" optional="true" label="Minimum gene length in number of nucleotides (-g, --gene_len)" help="It does not include the bases in the stop codon." />
91
92 <param name="glLinear" type="boolean" checked="false" label="Assuming a linear genome (-l, --linear)" help="No 'wrap-around' genes with part at the beginning of the sequence and the rest at the end of the sequence." />
93
94 <param name="glOrfCoords" type="data" format="glimmer_coords" optional="true" label="Coordinates file specifying a list of ORFs that should be scored separately, with no overlap rules (-L, --orf_coords)" help="The output with this option goes both to the .predict file and to the .detail file." />
95
96 <param name="glSeparateGenes" type="boolean" checked="false" label="Separate genes (-M, --separate_genes)" help="" />
97
98 <param name="glMaxOverlap" type="integer" value="" optional="true" label="Maximum overlap length (-o, --max_olap)" help="Overlaps of this many or fewer bases between genes are not regarded as overlaps." />
99
100 <param name="glStartProbs" type="text" value="" optional="true" label="Probability of different start codons (-P, --start_probs)" help="If no --codon_list option is given, then there should be 3 values: for atg, gtg and ttg, in that order. Sample format: -P 0.6,0.35,0.05. If --codon_list is specified without --start_probs, then each start codon is equally likely (which is very unusual)." />
101
102 <param name="glIgnoreScoreLen" type="integer" value="" optional="true" label="Consider any gene n or more bases long as a potential gene, regardless of its in-frame score (-q, --ignore_score_len)" help="Without this option, this value is calculated automatically to be the length such that the expected number of ORFs this long or longer in a random sequence of a million bases is one." />
103
104 <param name="glNoIndep" type="boolean" checked="false" label="Do not use the independent probability score column (-r, --no_indep)" help="Using this option will produce more short gene predictions." />
105
106 <param name="glThreshold" type="integer" value="" optional="true" label="Threshold score for consideration as a gene (-t, --threshold)" help="If the in-frame score ≥ n , then the region is given a number and considered a potential gene. Note this is the integer score in the column labelled 'InFrm' in the .detail file, not the decimal score in the column labelled 'Raw'." />
107
108 <param name="glExtend" type="boolean" checked="false" label="Also score ORFs that extend off the end of the sequence(s) (-X, --extend)" help="This option presumes that the sequence(s) is linear and not circular. Reported positions off the end of the sequence are the nearest positions in the correct reading frame. Note that this ignores any partial codons at the ends of a sequence. Suppose, for example, that a sequence is 998bp long and an ORF in reading frame +1 starts at position 601 and extends off the end of the sequence. Then the end of that gene/ORF will be reported at position 999, as if the stop codon were in positions 997 ... 999. This is true even if the last two characters of the sequence are, say, cc and cannot possibly be part of a stop codon." />
109
110 <param name="glTransTable" type="integer" value="" optional="true" label="Use GenBank translation table number n to specify stop codons (-z, --trans_table)" help="" />
111
112 <param name="glStopCodons" type="text" value="" optional="true" label="Specify allowable stop codons as a comma-separated list (-Z, --stop_codons)" help="Sample format: 'tag,tga,taa'. The default stop codons are tag, tga and taa." />
113 </inputs>
114
115 <outputs>
116 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
117 <data name="glDetail" format="txt" label="${tool.name} on ${on_string}: detail" />
118 <data name="glPredict" format="txt" label="${tool.name} on ${on_string}: predict" />
119 </outputs>
120
121 <tests>
122
123 </tests>
124 <help>
125 **What it does**
126
127 Read DNA sequences and predict genes in them using an Interpolated Context Model (ICM). Output details go to file *detail* and predictions go to file *predict*.
128
129 **License and citation**
130
131 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
132
133 .. _CRS4 Srl.: http://www.crs4.it/
134 .. _MIT license: http://opensource.org/licenses/MIT
135
136 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
137
138 .. |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*
139 .. _Cuccuru2013: http://orione.crs4.it/
140
141 This tool uses `Glimmer`_, which is licensed separately. Please cite |Delcher2007|_.
142
143 .. _Glimmer: http://ccb.jhu.edu/software/glimmer/index.shtml
144 .. |Delcher2007| replace:: Delcher, A. L., Bratke, K. A., Powers, E. C., Salzberg, S. L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. *Bioinformatics* 23(6), 673-679
145 .. _Delcher2007: http://bioinformatics.oxfordjournals.org/content/23/6/673
146 </help>
147 </tool>