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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit a712270ae9e703969bde0dc3268b047b6aab396f
author rnateam
date Sun, 03 Mar 2019 14:57:24 -0500
parents af2c31467ca0
children
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="metilene" name="metilene" version="0.2.6.1">
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3 <description>
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4 calling differentially methylated regions from bisulfite sequencing data
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5 </description>
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6 <requirements>
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7 <requirement type="package" version="0.2.6">metilene</requirement>
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8 <requirement type="package" version="3.5.1">r-base</requirement>
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9 <requirement type="package" version="2.24">bedtools</requirement>
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10 <requirement type="package" version="8.25">coreutils</requirement>
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11 </requirements>
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12 <stdio>
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13 <exit_code range=":-1"/>
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14 <exit_code range="1:" />
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15 </stdio>
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16 <version_command>echo "0.2.6"</version_command>
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17 <command><![CDATA[
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18 ## preprocessing
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19 ## generate metilene_g1_g2.input from multiple bedgraph files
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20 metilene_input.pl
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21 --in1 '$opt_in1'
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22 --in2 '$opt_in2'
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23 >/dev/null
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24 ##2>/dev/null
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25 &&
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26 ## metilene main program
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27 metilene
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28 -M $Options.opt_M
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29 -m $Options.opt_m
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30 -d $Options.opt_d
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31 -t \${GALAXY_SLOTS:-4}
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32 #if $B:
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33 -f 2
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34 -B "$B"
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35 #else:
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36 -f 1
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37 #end if
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38 #if $Options.Y:
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39 -Y $Options.Y
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40 #end if
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41 #if $Options.X:
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42 -X $Options.X
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43 #end if
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44
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45 -v $Options.opt_v
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46 metilene_g1_g2.input
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47 > '$output_bedlike'
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48 ##2> /dev/null
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49 &&
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50 ## postprocessing
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51 cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null
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52 &&
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53 ## write to job directory
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54 metilene_output.pl
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55 -q '$output_bedlike'
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56 -p 0.05
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57 -o ./metilene
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58 ##>/dev/null
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59 ##2>/dev/null
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60 ]]></command>
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61 <inputs>
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62 <!-- input bedgraph files 1 -->
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63 <param name="opt_in1" type="data" format="bed,bedgraph" multiple="true"
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64 label="Input group 1"
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65 help="Set of sorted bedgraph/bed input profiles of group 1" />
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66 <!-- input bedgraph files 2 -->
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67 <param name="opt_in2" type="data" format="bed,bedgraph" multiple="true"
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68 label="Input group 2"
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69 help="Set of sorted bedgraph/bed input profiles of group 2" />
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70
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71 <param argument="-B" type="data" format="bed" optional="True"
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72 label="BED file containing regions of interest"
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73 help="Regions that should be checked for differential methylation." />
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74
0
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75 <!-- Advanced parameters (folded) -->
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76 <section name="Options" title="Advanced Options" expanded="False">
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77 <param name="opt_M" type="integer" value="300"
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78 label="The allowed nt distance between two CpGs within a DMR"
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79 help="-M, --maxdist"/>
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80
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81 <param name="opt_m" type="integer" value="10"
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82 label="The minimum # of CpGs in a DMR"
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83 help="-m, --mincpgs"/>
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84
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85 <param argument="X" type="integer" value="" optional="True"
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86 label="Specify how many replicates must contain data for a certain CpG position in group 1"
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87 help="to estimate missing ones"/>
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88
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89 <param argument="Y" type="integer" value="" optional="True"
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90 label="Specify how many replicates must contain data for a certain CpG position in group 2"
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91 help="to estimate missing ones"/>
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92
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93 <param name="opt_d" type="float" value="0.1"
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94 label="The minimum mean methylation difference for calling DMRs"
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95 help="-d, --minMethDiff"/>
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96
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97 <param name="opt_v" type="float" value="0.7" label="Stringency of the valley filter (0.0 - 1.0)"
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98 help="-v, --valley">
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99 <validator type="in_range" min="0.0" max="1.0" message="Valley filter value must be in [0,1]." />
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100 </param>
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101 </section>
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102 </inputs>
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103 <outputs>
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104 <!-- finally: for bed-like use format=tabular -->
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105 <data format="tabular" name="output_bedlike"
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106 label="${tool.name} on ${on_string}" />
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107 <data format="bedgraph" name="output_bedgraph"
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108 label="${tool.name} bedgraph on ${on_string}" />
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109 <data format="bedgraph" name="output_qval_bedgraph"
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110 label="${tool.name} qval&lt;0.05 bedgraph on ${on_string}"
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111 from_work_dir="metilene_qval.0.05.bedgraph" />
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112 <data format="pdf" name="output_qval_pdf"
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113 label="${tool.name} qval&lt;0.05 plots on ${on_string}"
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114 from_work_dir="metilene_qval.0.05.pdf" />
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115 <data format="bedgraph" name="output_qval_out"
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116 label="${tool.name} qval&lt;0.05 out on ${on_string}"
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117 from_work_dir="metilene_qval.0.05.out" />
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118 </outputs>
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119 <tests>
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120 <test>
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121 <param name="opt_in1" value="example_S1.bedgraph,example_S2.bedgraph,example_S3.bedgraph,example_S4.bedgraph" />
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122 <param name="opt_in2" value="example_S5.bedgraph,example_S6.bedgraph,example_S7.bedgraph,example_S8.bedgraph" />
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123 <output name="output_bedlike" file="metilene.out" />
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124 </test>
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125 </tests>
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126 <help><![CDATA[
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127 **Fast and sensitive calling of differentially methylated regions
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128 from bisulfite sequencing data**
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129
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130 Detailed documentation of the stand-alone tool metilene is available at
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131 .. __: http://www.bioinf.uni-leipzig.de/Software/metilene/manual.pdf
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132
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133 The software metilene is available for download at
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134 .. __: http://www.bioinf.uni-leipzig.de/Software/metilene/
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135 ]]></help>
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136
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137 <citations>
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138 <citation type="bibtex">@Article{Juhling_Kretzmer_Bernhart-metil_Fast_and-2015,
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139 author = {Juhling, Frank and Kretzmer, Helene and Bernhart, Stephan
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140 H. and Otto, Christian and Stadler, Peter F. and Hoffmann,
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141 Steve},
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142 title = {metilene: {Fast} and sensitive calling of differentially
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143 methylated regions from bisulfite sequencing data},
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144 page = {[Epub ahead of print]},
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145 journal = {Genome Res},
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146 year = {2015},
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147 pmid = {26631489},
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148 doi = {10.1101/gr.196394.115},
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149 issn = {1088-9051},
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150 issn = {1549-5469}}</citation>
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151 </citations>
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152 </tool>