|
0
|
1 <tool id="cnmops" name="cn.mops" version="1.0.0">
|
|
|
2 <description>cnv caller</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="1.16.2">bioconductor-cn.mops</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command interpreter="Rscript">
|
|
|
7 cnmops.R $args_file
|
|
|
8 </command>
|
|
|
9 <configfiles>
|
|
|
10 <configfile name="args_file">target=$targetFile
|
|
|
11 padding=$padding
|
|
|
12 mapping_mode=$mapping_mode
|
|
|
13 #for $i in $inputs
|
|
|
14 bam=${i.input}
|
|
|
15 bam_bai=${i.input.metadata.bam_index}
|
|
|
16 #if str($i.label.value) != "":
|
|
|
17 bam_label=${$i.label.value}
|
|
|
18 #else
|
|
|
19 bam_label=${i.input.dataset.name}
|
|
|
20 #end if
|
|
|
21 #end for
|
|
|
22 output=$output
|
|
|
23 #if str($advanced_options.advanced_options_select) == "yes"
|
|
|
24 advanced_mode=TRUE
|
|
|
25 $advanced_options.prior_impact=$prior_impact
|
|
|
26 $advanced_options.cyc=$cyc
|
|
|
27 $advanced_options.norm=$norm
|
|
|
28 $advanced_options.norm_type=$norm_type
|
|
|
29 $advanced_options.upper_threshold=$upper_threshold
|
|
|
30 $advanced_options.lower_threshold=$lower_threshold
|
|
|
31 $advanced_options.min_width=$min_width
|
|
|
32 $advanced_options.seq_alg=$seq_alg
|
|
|
33 $advanced_options.min_read_count=$min_read_count
|
|
|
34 $advanced_options.use_median=$use_median
|
|
|
35 #end if
|
|
|
36 </configfile>
|
|
|
37 </configfiles>
|
|
|
38 <inputs>
|
|
|
39 <param format="bed" name="targetFile" type="data" label="Target regions (BED)">
|
|
|
40 <validator type="unspecified_build" />
|
|
|
41 </param>
|
|
|
42 <param name="padding" type="integer" value="100" label="Padding" help="Amount of padding (in bp) to add around each target region" />
|
|
|
43 <param name="mapping_mode" type="select" label="Mapping mode" help="Select whether the mapping algorithm was run using paired or unpaired reads">
|
|
|
44 <option value="paired" selected="true">paired</option>
|
|
|
45 <option value="unpaired">unpaired</option>
|
|
|
46 </param>
|
|
|
47 <repeat name="inputs" title="BAM" min="2" help="Need to add more files? Use controls below.">
|
|
|
48 <param format="bam" name="input" type="data" label="BAM file">
|
|
|
49 <options>
|
|
|
50 <filter type="data_meta" ref="targetFile" key="dbkey"/>
|
|
|
51 </options>
|
|
|
52 </param>
|
|
|
53 <param name="label" type="text" size="30" value="" label="Label" help="Label to use in the output. If not given, the dataset name will be used instead">
|
|
|
54 <validator type="regex" message="Spaces are not allowed">^\S*$</validator>
|
|
|
55 </param>
|
|
|
56 </repeat>
|
|
|
57
|
|
|
58 <!-- Advanced options -->
|
|
|
59 <conditional name="advanced_options">
|
|
|
60 <param name="advanced_options_select" type="select" label="Show advanced options">
|
|
|
61 <option value="yes">Yes</option>
|
|
|
62 <option value="no" selected="true">No</option>
|
|
|
63 </param>
|
|
|
64 <when value="yes">
|
|
|
65 <param name="prior_impact" type="integer" value="10" label="Prior impact" help="Positive real value that reflects how strong the prior assumption affects the result. The higher the value the more samples will be assumed to have copy number 2." />
|
|
|
66 <param name="cyc" type="integer" value="20" label="Cycles" help="Positive integer that sets the number of cycles for the algorithm. Usually after less than 15 cycles convergence is reached." />
|
|
|
67 <param name="norm" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Apply normalization" help="" />
|
|
|
68 <param name="norm_type" type="select" label="Normalization type" help="Mode of the normalization technique. Read counts will be scaled sample-wise.">
|
|
|
69 <option value="poisson" selected="true">poisson</option>
|
|
|
70 <option value="mean">mean</option>
|
|
|
71 <option value="min">min</option>
|
|
|
72 <option value="median">median</option>
|
|
|
73 <option value="quant">quant</option>
|
|
|
74 <option value="mode">mode</option>
|
|
|
75 </param>
|
|
|
76 <param name="upper_threshold" type="float" value="0.55" label="Cut-off for copy number gains" help="All CNV calling values above this value will be called as gain. The value should be set close to the log2 of the expected foldchange for copy number 3 or 4." />
|
|
|
77 <param name="lower_threshold" type="float" value="-0.8" label="Cut-off for copy number losses" help="All CNV calling values below this value will be called as loss. The value should be set close to the log2 of the expected foldchange for copy number 1 or 0." />
|
|
|
78 <param name="min_width" type="integer" value="5" label="Minimum width" help="Minimum number of segments a CNV should span." />
|
|
|
79 <param name="seq_alg" type="select" label="Segmentation algorithm" help="">
|
|
|
80 <option value="fast" selected="false">fast</option>
|
|
|
81 <option value="DNAcopy">DNAcopy</option>
|
|
|
82 </param>
|
|
|
83 <param name="min_read_count" type="integer" value="1" label="Minimum read count" help="If all samples are below this value the algorithm will return the prior knowledge. This prevents the algorithm from being applied to segments with very low coverage." />
|
|
|
84 <param name="use_median" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Use median" help="Whether median instead of mean of a target region should be used for the CNV call." />
|
|
|
85 </when>
|
|
|
86 <when value="no" />
|
|
|
87 </conditional>
|
|
|
88 </inputs>
|
|
|
89 <outputs>
|
|
|
90 <data format="bed" name="output" label="${tool.name} on ${on_string}" />
|
|
|
91 </outputs>
|
|
|
92 <help>
|
|
|
93
|
|
|
94 **What it does**
|
|
|
95
|
|
|
96 This tool uses cn.mops (Copy Number estimation by a Mixture Of PoissonS) to call copy number variations
|
|
|
97 and aberrations (CNVs and CNAs) from targeted next generation sequencing (NGS) data.
|
|
|
98
|
|
|
99 **Output format**
|
|
|
100
|
|
|
101 ========== ========================
|
|
|
102 Column Description
|
|
|
103 ---------- ------------------------
|
|
|
104 chr Chromosome
|
|
|
105 starts Start of CNV region
|
|
|
106 ends End of CNV region
|
|
|
107 sampleName Name of the sample with CNV
|
|
|
108 median Median value of CNV
|
|
|
109 mean Mean value of CNV
|
|
|
110 CN Copy number class (see below)
|
|
|
111 ========== ========================
|
|
|
112
|
|
|
113 Copy number classes are identified as follows::
|
|
|
114
|
|
|
115 CN2: normal copy number for diploid samples
|
|
|
116 CN1: heterozygous deletion
|
|
|
117 CN0: homozygous deletion
|
|
|
118 CN3 - CN8: amplifications
|
|
|
119
|
|
|
120 For non-tumor samples the highest copy number class is 8 - higher copy numbers have not been reported.
|
|
|
121 CN8 is expected to have 4 times as many reads (for times as high coverage) as CN2.
|
|
|
122 For tumor samples very high copy numbers have been observed (e.g. CN64),
|
|
|
123 therefore the parameters of cn.mops have to be adjusted to allow for high copy numbers.
|
|
|
124 A way to set the parameters is given in https://gist.github.com/gklambauer/8955203
|
|
|
125
|
|
|
126 **License and citation**
|
|
|
127
|
|
|
128 This Galaxy tool is Copyright © 2015 `CRS4 Srl.`_ and is released under the `MIT license`_.
|
|
|
129
|
|
|
130 .. _CRS4 Srl.: http://www.crs4.it/
|
|
|
131 .. _MIT license: http://opensource.org/licenses/MIT
|
|
|
132
|
|
|
133 You can use this tool only if you agree to the license terms of: `cn.mops`_.
|
|
|
134
|
|
|
135 .. _cn.mops: http://bioconductor.org/packages/release/bioc/html/cn.mops.html
|
|
|
136
|
|
|
137 If you use this tool, please cite:
|
|
|
138
|
|
|
139 - |Cuccuru2014|_
|
|
|
140 - |Klambauer2012|_.
|
|
|
141
|
|
|
142 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
|
|
|
143 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
|
|
|
144 .. |Klambauer2012| replace:: Klambauer, G., *et al.* (2012) cn.MOPS: Mixture of Poissons for Discovering Copy Number Variations in Next Generation Sequencing Data with a Low False Discovery Rate. *Nucleic Acids Research* 40, e69
|
|
|
145 .. _Klambauer2012: http://http://nar.oxfordjournals.org/content/40/9/e69
|
|
|
146 </help>
|
|
|
147 <citations>
|
|
|
148 <citation type="doi">10.1093/bioinformatics/btu135</citation>
|
|
|
149 <citation type="doi">10.1093/nar/gks003</citation>
|
|
|
150 </citations>
|
|
|
151 </tool>
|
