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1 <tool id="cnmops" name="cn.mops" version="1.0.0">
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2 <description>cnv caller</description>
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3 <requirements>
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2
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4 <requirement type="package" version="1.18.0">bioconductor-cn.mops</requirement>
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4
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5 </requirements>
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1
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6 <command interpreter="Rscript">
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7 cnmops.R $args_file
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8 </command>
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9 <configfiles>
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10 <configfile name="args_file">target=$targetFile
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11 padding=$padding
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12 mapping_mode=$mapping_mode
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13 #for $i in $inputs
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14 bam=${i.input}
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15 bam_bai=${i.input.metadata.bam_index}
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16 #if str($i.label.value) != "":
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17 bam_label=${$i.label.value}
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18 #else
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19 bam_label=${i.input.dataset.name}
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20 #end if
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21 #end for
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22 output=$output
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23 #if str($advanced_options.advanced_options_select) == "yes"
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24 advanced_mode=TRUE
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25 $advanced_options.prior_impact=$prior_impact
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26 $advanced_options.cyc=$cyc
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27 $advanced_options.norm=$norm
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28 $advanced_options.norm_type=$norm_type
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29 $advanced_options.upper_threshold=$upper_threshold
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30 $advanced_options.lower_threshold=$lower_threshold
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31 $advanced_options.min_width=$min_width
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32 $advanced_options.seq_alg=$seq_alg
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33 $advanced_options.min_read_count=$min_read_count
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34 $advanced_options.use_median=$use_median
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35 #end if
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36 </configfile>
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37 </configfiles>
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38 <inputs>
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39 <param format="bed" name="targetFile" type="data" label="Target regions (BED)">
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40 <validator type="unspecified_build" />
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41 </param>
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42 <param name="padding" type="integer" value="100" label="Padding" help="Amount of padding (in bp) to add around each target region" />
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43 <param name="mapping_mode" type="select" label="Mapping mode" help="Select whether the mapping algorithm was run using paired or unpaired reads">
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44 <option value="paired" selected="true">paired</option>
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45 <option value="unpaired">unpaired</option>
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46 </param>
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47 <repeat name="inputs" title="BAM" min="2" help="Need to add more files? Use controls below.">
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48 <param format="bam" name="input" type="data" label="BAM file">
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49 <options>
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50 <filter type="data_meta" ref="targetFile" key="dbkey"/>
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51 </options>
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52 </param>
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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">
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54 <validator type="regex" message="Spaces are not allowed">^\S*$</validator>
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55 </param>
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56 </repeat>
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57
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58 <!-- Advanced options -->
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59 <conditional name="advanced_options">
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60 <param name="advanced_options_select" type="select" label="Show advanced options">
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61 <option value="yes">Yes</option>
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62 <option value="no" selected="true">No</option>
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63 </param>
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64 <when value="yes">
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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." />
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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." />
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67 <param name="norm" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Apply normalization" help="" />
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68 <param name="norm_type" type="select" label="Normalization type" help="Mode of the normalization technique. Read counts will be scaled sample-wise.">
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69 <option value="poisson" selected="true">poisson</option>
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70 <option value="mean">mean</option>
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71 <option value="min">min</option>
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72 <option value="median">median</option>
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73 <option value="quant">quant</option>
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74 <option value="mode">mode</option>
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75 </param>
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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." />
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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." />
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78 <param name="min_width" type="integer" value="5" label="Minimum width" help="Minimum number of segments a CNV should span." />
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79 <param name="seq_alg" type="select" label="Segmentation algorithm" help="">
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80 <option value="fast" selected="false">fast</option>
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81 <option value="DNAcopy">DNAcopy</option>
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82 </param>
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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." />
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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." />
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85 </when>
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86 <when value="no" />
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87 </conditional>
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88 </inputs>
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89 <outputs>
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90 <data format="bed" name="output" label="${tool.name} on ${on_string}" />
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91 </outputs>
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92 <help>
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93
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94 **What it does**
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95
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96 This tool uses cn.mops (Copy Number estimation by a Mixture Of PoissonS) to call copy number variations
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97 and aberrations (CNVs and CNAs) from targeted next generation sequencing (NGS) data.
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98
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99 **Output format**
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100
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101 ========== ========================
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102 Column Description
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103 ---------- ------------------------
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104 chr Chromosome
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105 starts Start of CNV region
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106 ends End of CNV region
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107 sampleName Name of the sample with CNV
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108 median Median value of CNV
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109 mean Mean value of CNV
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110 CN Copy number class (see below)
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111 ========== ========================
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112
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113 Copy number classes are identified as follows::
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114
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115 CN2: normal copy number for diploid samples
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116 CN1: heterozygous deletion
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117 CN0: homozygous deletion
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118 CN3 - CN8: amplifications
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119
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120 For non-tumor samples the highest copy number class is 8 - higher copy numbers have not been reported.
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121 CN8 is expected to have 4 times as many reads (for times as high coverage) as CN2.
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122 For tumor samples very high copy numbers have been observed (e.g. CN64),
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123 therefore the parameters of cn.mops have to be adjusted to allow for high copy numbers.
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124 A way to set the parameters is given in https://gist.github.com/gklambauer/8955203
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125
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126 **License and citation**
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127
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128 This Galaxy tool is Copyright © 2015 `CRS4 Srl.`_ and is released under the `MIT license`_.
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129
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130 .. _CRS4 Srl.: http://www.crs4.it/
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131 .. _MIT license: http://opensource.org/licenses/MIT
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132
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133 You can use this tool only if you agree to the license terms of: `cn.mops`_.
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134
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135 .. _cn.mops: http://bioconductor.org/packages/release/bioc/html/cn.mops.html
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136
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137 If you use this tool, please cite:
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138
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139 - |Cuccuru2014|_
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140 - |Klambauer2012|_.
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141
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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
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143 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
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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
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145 .. _Klambauer2012: http://http://nar.oxfordjournals.org/content/40/9/e69
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146 </help>
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147 <citations>
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148 <citation type="doi">10.1093/bioinformatics/btu135</citation>
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149 <citation type="doi">10.1093/nar/gks003</citation>
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150 </citations>
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151 </tool>
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