Mercurial > repos > rnateam > methylkit

annotate methylkit.xml @ 0:a8705df7c57f draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
author rnateam
date Wed, 21 Dec 2016 17:30:57 -0500
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0
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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1 <tool id="methylkit" name="methylKit" version="0.99.2">
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2 <description>DNA methylation analysis and annotation</description>
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3 <macros>
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4 <macro name="differential_methylation">
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5 <param name="overdispersion" type="select"
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6 label="overdispersion"
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7 help="if set to 'none' (default), no overdispersion
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8 correction will be attempted. 'MN' applies a scaling
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9 parameter to variance estimated by the model.
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10 If set to 'shrinkMN' (experimental parameter),
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11 scaling parameter will be shrunk towards a common value">
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12 <option value="none" selected="True">
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13 none
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14 </option>
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15 <option value="MN">
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16 MN
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17 </option>
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18 <option value="shrinkMN">
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19 shrinkMN
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20 </option>
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21 </param>
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22 <param name="adjust" type="select"
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23 label="adjust"
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24 help="different methods to correct the p-values
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25 for multiple testing (default: SLIM).">
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26 <option value="SLIM" selected="True">
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27 SLIM
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28 </option>
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29 <option value="holm">
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30 holm
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31 </option>
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32 <option value="hochberg">
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33 hochberg
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34 </option>
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35 <option value="hommel">
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36 hommel
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37 </option>
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38 <option value="bonferroni">
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39 bonferroni
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40 </option>
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41 <option value="BH">
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42 BH
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43 </option>
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44 <option value="BY">
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45 BY
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46 </option>
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47 <option value="fdr">
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48 fdr
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49 </option>
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50 <option value="none">
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51 none
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52 </option>
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53 <option value="qvalue">
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54 qvalue
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55 </option>
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56 </param>
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57 <param name="effect" type="select"
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58 label="effect"
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59 help="method to calculate the mean methylation different
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60 between groups using read coverage as weights (default: wmean).
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61 When set to 'mean', the generic mean is applied and when
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62 set to 'predicted', predicted means from the logistic
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63 regression model is used for calculating the effect.">
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64 <option value="wmean" selected="True">
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65 wmean
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66 </option>
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67 <option value="mean">
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68 mean
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69 </option>
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70 <option value="predicted">
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71 predicted
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72 </option>
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73 </param>
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74 <param name="test" type="select"
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75 label="test"
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76 help="the statistical test used to determine
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77 the methylation differences (default: Chisq-test).
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78 The F-test can be chosen
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79 if overdispersion control is applied.">
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80 <option value="Chisq" selected="True">
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81 Chisq
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82 </option>
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83 <option value="F">
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84 F
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85 </option>
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86 </param>
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87 <param name="qvalue_cutoff" type="float"
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88 value="0.01" label="qvalue.cutoff"
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89 help="cutoff for qvalue of differential methylation statistic (default:0.01)">
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90 <validator type="in_range"
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91 message="Minimum 0 and maximum 1" min="0" max="1"/>
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92 </param>
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93 <param name="meth_cutoff" type="float"
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diff changeset
94 value="25" label="meth.cutoff"
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95 help="cutoff for absolute value of methylation percentage change between test and control (default:25)">
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96 <validator type="in_range"
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diff changeset
97 message="Minimum 0 and maximum 100" min="0" max="100"/>
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98 </param>
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diff changeset
99 <param name="type" type="select"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
100 label="type"
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diff changeset
101 help="For retrieving
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102 hyper-methylated regions/bases type='hyper',
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diff changeset
103 for hypo-methylated type='hypo' (default:'all')">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
104 <option value="all" selected="True">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
105 all
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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106 </option>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
107 <option value="hyper">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
108 hyper
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109 </option>
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diff changeset
110 <option value="hypo">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
111 hypo
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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112 </option>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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113 </param>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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114 </macro>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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115 <macro name="clustering">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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116 <param name="dist" type="select"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
117 label="dist"
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diff changeset
118 help="the distance measure to be used.
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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119 (default: correlation)">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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120 <option value="correlation" selected="True">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
121 correlation
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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122 </option>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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123 <option value="euclidean">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
124 euclidean
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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125 </option>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
126 <option value="maximum">
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diff changeset
127 maximum
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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128 </option>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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129 <option value="manhattan">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
130 manhattan
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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131 </option>
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132 <option value="canberra">
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diff changeset
133 canberra
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134 </option>
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135 <option value="binary">
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diff changeset
136 binary
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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137 </option>
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138 <option value="minkowski">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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139 minkowski
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140 </option>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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141 </param>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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142 <param name="method" type="select"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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143 label="method"
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144 help="the agglomeration method to be used.
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145 (default: ward)">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
146 <option value="ward" selected="True">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
147 ward
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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148 </option>
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diff changeset
149 <option value="single">
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diff changeset
150 single
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
151 </option>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
152 <option value="complete">
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diff changeset
153 complete
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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154 </option>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
155 <option value="average">
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diff changeset
156 average
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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157 </option>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
158 <option value="mcquitty">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
159 mcquitty
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diff changeset
160 </option>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
161 <option value="median">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
162 median
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163 </option>
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diff changeset
164 <option value="centroid">
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165 centroid
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166 </option>
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167 </param>
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diff changeset
168 </macro>
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169 </macros>
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170 <requirements>
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171 <requirement type="package" version="0.99.2">bioconductor-methylkit</requirement>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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172 </requirements>
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173 <stdio>
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174 <regex match="Execution halted"
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diff changeset
175 source="both"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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176 level="fatal"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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177 description="Execution halted." />
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178 <regex match="Input-Error 01"
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diff changeset
179 source="both"
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180 level="fatal"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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181 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
182 <regex match="Error in"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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183 source="both"
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184 level="fatal"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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185 description="An undefined error occured, please check your intput carefully and contact your administrator." />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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186 </stdio>
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187 <command>
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188 <![CDATA[
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189 Rscript $script_file
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190 ]]>
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191 </command>
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192 <configfiles>
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193 <configfile name="script_file">
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194 library("methylKit")
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195
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196 test_files = list()
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197 control_files = list()
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198
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199 test_ids = list()
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200 control_ids = list()
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201
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202 #for $i, $s in enumerate( $test_series )
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203 test_ids[${i}+1] = paste("test ", ${i}+1, sep="")
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204 test_files[${i}+1] = "${s.input.file_name}"
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205 #end for
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206
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207 #for $i, $s in enumerate( $control_series )
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208 control_ids[${i}+1] = paste("control ", ${i}+1, sep="")
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209 control_files[${i}+1] = "${s.input.file_name}"
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210 #end for
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211
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212 input_files = append(test_files, control_files)
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213 sample_ids = append(test_ids, control_ids)
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214 treatment_tag = c(rep.int(1, length(test_ids)), rep.int(0, length(control_ids)))
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215
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216 myobj=methRead(input_files, sample.id=sample_ids, assembly="${assembly}",
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217 pipeline="${pipeline}", treatment=treatment_tag)
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218
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219 pdf('output_statistics.pdf')
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220 for (obj in myobj){
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221 getMethylationStats(obj,plot=TRUE,both.strands=FALSE)
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222 getCoverageStats(obj,plot=TRUE,both.strands=FALSE)
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223 }
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224 devname = dev.off()
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225
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226 ## unite function
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227 methidh=unite(myobj)
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228
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229 pdf("output_correlation.pdf")
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230 getCorrelation(object = methidh, plot=TRUE, method = "${correlation}")
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231 devname = dev.off()
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232
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233 #if $input_type.choice in ["all", "differential_methylation"]:
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234 ## the last two arguments slim, weighted.mean
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235 ## have the redundant counterparts in effect and adjust,
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236 ## so turning them off to avoide the possible conflict.
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237 myDiff = calculateDiffMeth(methidh, overdispersion="${input_type.overdispersion}",
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238 adjust="${input_type.adjust}", effect="${input_type.effect}", test="${input_type.test}",
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239 slim=FALSE, weighted.mean=FALSE)
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240
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241 bedgraph(myDiff, file.name="output_myDiff.bedgraph", col.name="meth.diff",
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242 unmeth=FALSE, log.transform=FALSE, negative=FALSE, add.on="")
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243
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244 MethPerChr = diffMethPerChr(myDiff, plot=FALSE,
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245 qvalue.cutoff=${input_type.qvalue_cutoff},
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246 meth.cutoff=${input_type.meth_cutoff})
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247 write.table(MethPerChr, sep="\t", row.names=FALSE, quote=FALSE, file="output_MethPerChr.tsv")
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248
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249 MethylDiff = getMethylDiff(myDiff, difference=${input_type.meth_cutoff},
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250 qvalue=${input_type.qvalue_cutoff}, type="${input_type.type}")
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251 bedgraph(MethylDiff, file.name="output_MethylDiff.bedgraph", col.name="meth.diff",
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252 unmeth=FALSE,log.transform=FALSE,negative=FALSE,add.on="")
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253 #end if
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254
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255 #if $input_type.choice in ["all", "clustering"]:
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256 pdf( "output_clustering.pdf" )
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257 methClust = clusterSamples(methidh, dist="${input_type.dist}", method="${input_type.method}")
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258 devname = dev.off()
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259
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260 pdf( "output_PCA.pdf" )
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261 PCASamples(methidh)
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262 devname = dev.off()
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263 #end if
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264
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265 #if $input_type.choice in ["all", "segmentation"]:
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266 ## methSeg works for methylRaw or methylDiff with resolution region,
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267 ## so methylBase has to be tiled before
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268 tileRaw = tileMethylCounts(myobj[[1]])
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269 tileBase = tileMethylCounts(methidh)
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270 tileDiff = calculateDiffMeth(tileBase)
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271
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272 ## methseg generates Granges
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273 segRaw = methSeg(tileRaw, diagnostic.plot = FALSE)
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274 segDiff = methSeg(tileDiff, diagnostic.plot = FALSE)
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275
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276 ## and can be exported as BED
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277 methSeg2bed(segments = segRaw, filename = "output_seg_raw.bed")
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278 methSeg2bed(segments = segDiff, filename = "output_seg_diff.bed")
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279 #end if
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280 </configfile>
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281 </configfiles>
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282 <inputs>
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283 <repeat name="test_series" title="Test samples" min="1">
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284 <param name="input" type="data" format="tabular" label="Add a file"
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285 help="Such input file may be obtained from AMP pipeline for aligning RRBS reads.">
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286 <validator type="unspecified_build" />
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287 </param>
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288 </repeat>
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289 <repeat name="control_series" title="Control samples" min="1">
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290 <param name="input" type="data" format="tabular" label="Add a file"
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291 help="Such input file may be obtained from AMP pipeline for aligning RRBS reads." >
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292 <validator type="unspecified_build" />
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293 </param>
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294 </repeat>
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295 <param name="assembly" type="text"
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296 value="hg18" label="assembly"
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297 help="A string that defines the genome assembly such as
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298 hg18, mm9 (default: hg18).">
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299 </param>
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300 <param name="correlation" type="select"
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301 label="correlation"
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302 help="correlation method (default: pearson)">
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303 <option value="pearson" selected="True">
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304 pearson
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305 </option>
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306 <option value="kendall">
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307 kendall
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308 </option>
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309 <option value="spearman">
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310 spearman
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311 </option>
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312 </param>
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313 <param name="pipeline" type="select"
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314 label="pipeline"
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315 help="name of the alignment pipeline (default: amp)">
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316 <option value="amp" selected="True">
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317 amp
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318 </option>
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319 <option value="bismark">
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320 bismark
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321 </option>
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322 <option value="bismarkCoverage">
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323 bismarkCoverage
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324 </option>
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325 <option value="bismarkCytosineReport">
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326 bismarkCytosineReport
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327 </option>
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328 </param>
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329 <conditional name="input_type">
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330 <param name="choice" type="select"
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331 label="analysis to carry out:"
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332 help="The analysis you wish to carry out.">
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333 <option value="all" selected="True">
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334 All provided analysis
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335 </option>
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336 <option value="differential_methylation">
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337 Differential methylation
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338 </option>
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339 <option value="clustering">
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340 Clustering
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341 </option>
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342 <option value="segmentation">
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343 Segmentation
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344 </option>
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345 </param>
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346 <when value="all">
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347 <expand macro="differential_methylation" />
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348 <expand macro="clustering" />
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349 </when>
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350 <when value="differential_methylation">
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351 <expand macro="differential_methylation" />
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352 </when>
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353 <when value="clustering">
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354 <expand macro="clustering" />
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355 </when>
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356 <when value="segmentation" />
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357 </conditional>
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358 </inputs>
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359 <outputs>
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360 <data name="output_statistics" format="pdf"
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361 from_work_dir="output_statistics.pdf"
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362 label="${tool.name} on ${on_string}: CpG statistics">
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363 </data>
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364
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365 <data name="output_correlation" format="pdf"
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366 from_work_dir="output_correlation.pdf"
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367 label="${tool.name} on ${on_string}: correlation between samples">
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368 </data>
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369
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370 <data name="output_myDiff" format="bedgraph"
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371 from_work_dir="output_myDiff.bedgraph"
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372 label="${tool.name} on ${on_string}: differential methylation">
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373 <filter>input_type['choice'] in ['all', 'differential_methylation']</filter>
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374 </data>
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375
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376 <data name="output_MethylDiff" format="bedgraph"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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377 from_work_dir="output_MethylDiff.bedgraph"
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378 label="${tool.name} on ${on_string}: differential methylation - subset">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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379 <filter>input_type['choice'] in ['all', 'differential_methylation']</filter>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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380 </data>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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381
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382 <data name="output_MethPerChr" format="tabular"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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383 from_work_dir="output_MethPerChr.tsv"
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diff changeset
384 label="${tool.name} on ${on_string}: number of hyper/hypo sites">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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385 <filter>input_type['choice'] in ['all', 'differential_methylation']</filter>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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386 </data>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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387
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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388 <data name="output_clustering" format="pdf"
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389 from_work_dir="output_clustering.pdf"
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390 label="${tool.name} on ${on_string}: hierarchical clustering">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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391 <filter>input_type['choice'] in ['all', 'clustering']</filter>
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392 </data>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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393
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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394 <data name="output_PCA" format="pdf"
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395 from_work_dir="output_PCA.pdf"
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396 label="${tool.name} on ${on_string}: PCA">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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397 <filter>input_type['choice'] in ['all', 'clustering']</filter>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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398 </data>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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399
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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400 <data name="output_seg_raw" format="bed"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
401 from_work_dir="output_seg_raw.bed"
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diff changeset
402 label="${tool.name} on ${on_string}: methylation segment">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
403 <filter>input_type['choice'] in ['all', 'segmentation']</filter>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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404 </data>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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405
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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406 <data name="output_seg_diff" format="bed"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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407 from_work_dir="output_seg_diff.bed"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
408 label="${tool.name} on ${on_string}: differential methylation segment">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
409 <filter>input_type['choice'] in ['all', 'segmentation']</filter>
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410 </data>
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411 </outputs>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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412 <tests>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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413 <test>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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414 <repeat name="test_series">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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415 <param name="input" value="input_test1.myCpG.txt" dbkey="hg18" ftype="tabular" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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416 </repeat>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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417 <repeat name="test_series">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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418 <param name="input" value="input_test2.myCpG.txt" dbkey="hg18" ftype="tabular" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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419 </repeat>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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420 <repeat name="control_series">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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421 <param name="input" value="input_control1.myCpG.txt" dbkey="hg18" ftype="tabular" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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422 </repeat>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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423 <repeat name="control_series">
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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424 <param name="input" value="input_control2.myCpG.txt" dbkey="hg18" ftype="tabular" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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425 </repeat>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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426 <param name="assembly" value="hg18" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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427 <param name="correlation" value="pearson" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
428 <param name="pipeline" value="amp" />
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429 <param name="choice" value="all" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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430 <param name="overdispersion" value="none" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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431 <param name="adjust" value="SLIM" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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432 <param name="effect" value="wmean" />
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433 <param name="test" value="Chisq" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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434 <param name="qvalue_cutoff" value="0.01" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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435 <param name="meth_cutoff" value="25" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
436 <param name="type" value="all" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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437 <param name="dist" value="correlation" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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438 <param name="method" value="ward" />
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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439 <output name="output_statistics" file="output_statistics.pdf"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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440 ftype="pdf" compare="sim_size"/>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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441 <output name="output_correlation" file="output_correlation.pdf"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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442 ftype="pdf" compare="sim_size"/>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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443 <output name="output_myDiff" file="output_myDiff.bedgraph"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
444 ftype="bedgraph"/>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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445 <output name="output_MethPerChr" file="output_MethPerChr.tsv"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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446 ftype="tabular"/>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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447 <output name="output_MethylDiff" file="output_MethylDiff.bedgraph"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
448 ftype="bedgraph"/>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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449 <output name="output_clustering" file="output_clustering.pdf"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
450 ftype="pdf" compare="sim_size"/>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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451 <output name="output_PCA" file="output_PCA.pdf"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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452 ftype="pdf" compare="sim_size"/>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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453 <output name="output_seg_raw" file="output_seg_raw.bed"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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454 ftype="bed"/>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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455 <output name="output_seg_diff" file="output_seg_diff.bed"
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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diff changeset
456 ftype="bed"/>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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457 </test>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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458 </tests>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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459 <help>
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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460 <![CDATA[
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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461 .. class:: infomark
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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462
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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463 **What it does**
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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464
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465 `methylKit`_ is an R package for DNA methylation analysis and annotation
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466 from high-throughput bisulfite sequencing.
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467 The package is designed to deal with sequencing data from RRBS and
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468 its variants, but also target-capture methods such as Agilent SureSelect
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469 methyl-seq. In addition, methylKit can deal with base-pair resolution data
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470 for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome
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471 bisulfite sequencing data if proper input format is provided.
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472
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473 .. _methylKit: https://github.com/al2na/methylKit
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474
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475 The Galaxy tool enables three types of analysis:
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476 * differential methylation
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477 * clustering
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478 * segmentation
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479
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480 The user can choose to run all provided analysis or run an individual one.
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481
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482 .. class:: infomark
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483
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484 **Input**
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485
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486 Typically, bisulfite converted reads are aligned to the genome and %
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487 methylation value per base is calculated by processing alignments.
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488 methylKit takes that % methylation value per base information as input.
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489 Such input file may be obtained from `AMP`_ pipeline
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490 for aligning RRBS reads. A typical input file looks like this::
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491
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492
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493 chrBase chr base strand coverage freqC freqT
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494
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495 chr21.9764539 chr21 9764539 R 12 25.00 75.00
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496
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497 chr21.9764513 chr21 9764513 F 12 0.00 100.00
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498
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499
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500 .. _AMP: http://code.google.com/p/amp-errbs/
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501
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502 .. class:: infomark
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503
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504 **Output**
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505
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506 The outputs from differential methylation
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507 * ``differential methylation``: The `bedgraph`_ file contains differentially methylated bases/regions and the corresponding statistics.
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508 * ``differential methylation - subset``: The bedgraph file contains the subset of differentially methylated bases/regions that satisfies the user defined thresholds with qvalue.cutoff and meth.cutoff.
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509 * ``number of hyper/hypo sites``: The tabular file contains number of hyper/hypo methylated regions/bases.
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510
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511 .. _bedgraph: https://genome.ucsc.edu/goldenpath/help/bedgraph.html
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512
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513 The outputs from clustering
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514 * ``hierarchical clustering``: The figure shows hierarchical clustering using methylation data.
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515 * ``PCA``: The figure shows principal components analysis of methylation data.
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516
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517 The output from segmentation
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518 * ``methylation segment``: The `bed`_ file contains the profile of methylation segment.
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519 * ``differential methylation segment``: The bed file contains the profile of differential methylation segment.
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520
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521 .. _bed: https://genome.ucsc.edu/FAQ/FAQformat#format1
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522 ]]>
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523 </help>
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524 <citations>
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525 <citation type="doi">10.1186/gb-2012-13-10-r87</citation>
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526 </citations>
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527 </tool>