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annotate epicseg.xml @ 0:6260e42c7d49 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
author rnateam
date Wed, 07 Mar 2018 16:56:29 -0500
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6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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1 <tool id="epicseg_segment" name="EpiCSeg - Chromatin segmentation" version="@VERSION_STRING@">
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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2 <macros>
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3 <import>macros.xml</import>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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4 </macros>
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5 <expand macro="requirements" />
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6 <command detect_errors="exit_code"><![CDATA[
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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8 mkdir -p '${ report.files_path }' &&
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9
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10 ## Acquire the count matrices
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11 #for $d, $dataset in enumerate( $datasets ):
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12 #for $i, $mark in enumerate( $dataset.marks ):
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13 ln -s -f '${mark.reads}' '${d}_${i}.bam' &&
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14 ln -s -f '${mark.reads.metadata.bam_index}' '${d}_${i}.bam.bai' &&
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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15 #end for
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16
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17 Rscript '${__tool_directory__}/epicseg.R' getcounts
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18 --binsize $binsize --nthreads \${GALAXY_SLOTS:-2}
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19 --regions '$regions' --target '${d}.tab'
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21 #for $i, $mark in enumerate( $dataset.marks):
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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22 --mark '${mark.label}:${d}_${i}.bam' --mapq ${mark.mapq}
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23 ${mark.pairedend} --shift ${mark.shift}
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24 #end for
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25
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26 &&
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27 #end for
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28
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29 ## Normalize the datasets
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30 #if len( $datasets ) == 1:
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31 ln -s 0.tab 0_norm.tab
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32 #else:
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33 Rscript '${__tool_directory__}/epicseg.R' normalizecounts
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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34 --nthreads \${GALAXY_SLOTS:-2}
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35
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36 #for $d, $dataset in enumerate( $datasets)
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37 --counts '${d}.tab'
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38 #end for
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39
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40 #end if
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41
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42 &&
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43
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44 ## Segment
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45 Rscript '${__tool_directory__}/epicseg.R' segment --regions '$regions'
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46 --nstates $nstates --nthreads \${GALAXY_SLOTS:-2}
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47 --outdir '${report.files_path}'
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48 #for $d, $dataset in enumerate( $datasets ):
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49 --counts '${dataset.name}:${d}_norm.tab'
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50 #end for
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51
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52 --maxiter $maxiter
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53
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54 #for $annot in $annots:
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55 --annot '${annot.name}:${annot.file}'
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56 #end for#
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57 &&
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58 cp ${report.files_path}/report.html . &&
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59 cp ${report.files_path}/segmentation*.bed .
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60 ]]></command>
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61 <inputs>
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62 <param type="data" name="regions" format="bed" label="Regions in BED format"
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63 help="BED file with the genomic regions of interest.
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64 These regions will be automatically partitioned into
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65 smaller, consecutive bins. Only the first three fields
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66 in the file matter. If the region lengths are not
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67 multiples of the given binsize a new bed file will be
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68 produced where each coordinate is a multiple of binsize."/>
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69 <param type="integer" name="binsize" min="0" value="200"
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70 help="Size of a bin in base pairs. Each given region will
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71 be partitioned into bins of this size."/>
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72 <repeat name="datasets" title="Datasets"
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73 help="Chromatin segmentation may be performed across one or more
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74 datasets (e.g. cell-types or conditions) each
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75 of which consisting
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76 of a set of chromatin marks (e.g. H3K4me3).
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77 If multiple datasets are used,
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78 they must share the same set of chromatin marks.">
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79 <param type="text" name="name" label="Dataset name"
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80 value="Treatment" />
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81 <repeat name="marks" title="Chromatin mark">
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82 <param type="text" name="label" label="Mark name"
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83 value="H3K4me3" />
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84 <param type="data" name="reads" label="Reads in BAM format"
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85 format="bam"
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86 help="BAM file containing the read alignments for
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87 the corresponding chromatin mark.
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88 If the same mark name is used multiple times,
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89 the associated reads will be treated as replicates
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90 and collapsed into one experiment."/>
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91 <param type="integer" name="mapq" min="0" value="0"
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92 help="Minimum mapping quality for the reads (see the
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93 bam format specification for the mapq field).
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94 Only reads with the mapq field above or equal
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95 to the specified value will be considered."/>
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96 <param type="boolean" name="pairedend"
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97 truevalue="--pairedend TRUE" falsevalue="--pairedend FALSE"
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98 help="Set this option to TRUE or FALSE to activate or
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99 deactivate the paired-end mode. Only read pairs
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100 where both ends are mapped will be considered and
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101 assigned to the bin where the midpoint of the
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102 read pair is located. If this flag is set, the
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103 `shift` option will be ignored."/>
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104 <param type="integer" name="shift" value="75"
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105 help="Shift the reads in the 5' direction by a fixed
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106 number of base pairs. The read will be assigned
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107 to the bin where the shifted 5' end of the read
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108 is located. This option will be ignored in
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109 paired-end mode."/>
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110 </repeat>
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111 </repeat>
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112
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113
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114 <param type="integer" name="nstates" label="Number of states"
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115 min="0" value="5"
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116 help="Number of chromatin states."/>
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117 <param type="integer" name="maxiter" value="200"
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118 help="Maximum number of iterations during training."/>
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119
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120 <repeat name="annots" title="Annotation"
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121 help="(Optional) Annotation tracks might be overlayed
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122 with the segmentation results.">
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123 <param type="text" name="name" label="Annotation name"
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124 value="genes" />
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125 <param type="data" name="file" label="Annotation"
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126 format="bed"
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127 help="BED-file containing the annotation. For example,
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128 gene annotation or CpG-islands." />
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129 </repeat>
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130 </inputs>
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131 <outputs>
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132 <data name="report" format="html" from_work_dir='report.html' >
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133 <discover_datasets pattern="segmentation" format="bed"
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134 visible="true" />
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135 </data>
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136 </outputs>
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137 <tests>
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138 <test>
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139 <!-- 1 Dataset w/o annotation -->
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140 <param name="regions" value="chr1.bed"/>
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141 <repeat name="datasets">
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142 <param name="name" value="DS1" />
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143 <repeat name="marks">
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144 <param name="label" value="H3K4me3" />
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145 <param name="reads" value="chr1_h1hesc_h3k4me3.bam" />
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146 <param name="mapq" value="0"/>
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147 <param name="pairedend" value="--pairedend FALSE"/>
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148 <param name="shift" value="75"/>
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149 </repeat>
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150 <repeat name="marks">
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151 <param name="label" value="H3K4me1" />
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152 <param name="reads" value="chr1_h1hesc_h3k4me1.bam" />
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153 <param name="mapq" value="0"/>
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154 <param name="pairedend" value="--pairedend FALSE"/>
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155 <param name="shift" value="75"/>
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156 </repeat>
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157 <repeat name="marks">
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158 <param name="label" value="H3K4me1" />
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159 <param name="reads" value="chr1_h1hesc_h3k4me1_rep2.bam" />
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160 <param name="mapq" value="0"/>
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161 <param name="pairedend" value="--pairedend FALSE"/>
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162 <param name="shift" value="75"/>
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163 </repeat>
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164 <repeat name="marks">
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165 <param name="label" value="H4K27me3" />
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166 <param name="reads" value="chr1_h1hesc_h3k27me3.bam" />
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167 <param name="mapq" value="0"/>
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168 <param name="pairedend" value="--pairedend FALSE"/>
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169 <param name="shift" value="75"/>
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170 </repeat>
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171 </repeat>
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172 <param name="binsize" value="200" />
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173 <param name="nstates" value="5" />
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174 <output name="report" file="report_1ds.html"/>
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175 </test>
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176 <test>
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177 <!-- 1 Dataset with annotation -->
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178 <param name="regions" value="chr1.bed"/>
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179 <repeat name="datasets">
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180 <param name="name" value="DS1" />
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181 <repeat name="marks">
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182 <param name="label" value="H3K4me3" />
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183 <param name="reads" value="chr1_h1hesc_h3k4me3.bam" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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184 <param name="mapq" value="0"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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185 <param name="pairedend" value="--pairedend FALSE"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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186 <param name="shift" value="75"/>
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187 </repeat>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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188 <repeat name="marks">
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189 <param name="label" value="H3K4me1" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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190 <param name="reads" value="chr1_h1hesc_h3k4me1.bam" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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191 <param name="mapq" value="0"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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192 <param name="pairedend" value="--pairedend FALSE"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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193 <param name="shift" value="75"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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194 </repeat>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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195 <repeat name="marks">
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196 <param name="label" value="H3K4me1" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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197 <param name="reads" value="chr1_h1hesc_h3k4me1_rep2.bam" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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198 <param name="mapq" value="0"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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199 <param name="pairedend" value="--pairedend FALSE"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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200 <param name="shift" value="75"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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201 </repeat>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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202 <repeat name="marks">
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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203 <param name="label" value="H4K27me3" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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204 <param name="reads" value="chr1_h1hesc_h3k27me3.bam" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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205 <param name="mapq" value="0"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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206 <param name="pairedend" value="--pairedend FALSE"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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207 <param name="shift" value="75"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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208 </repeat>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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209 </repeat>
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210 <param name="binsize" value="200" />
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211 <param name="nstates" value="5" />
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212 <repeat name="annots">
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213 <param name="name" value="cpg" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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214 <param name="file" value="cpgIslandExt.hg19.bed" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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215 </repeat>
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216 <output name="report" file="report_1ds_w_annot.html"/>
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217 </test>
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218
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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219 <test>
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220 <!-- 2 Datasets w/o annotation -->
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221 <param name="regions" value="chr1.bed"/>
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222 <repeat name="datasets">
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223 <param name="name" value="DS1" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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224 <repeat name="marks">
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225 <param name="label" value="H3K4me3" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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226 <param name="reads" value="chr1_h1hesc_h3k4me3.bam" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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227 <param name="mapq" value="0"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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228 <param name="pairedend" value="--pairedend FALSE"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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229 <param name="shift" value="75"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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230 </repeat>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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231 <repeat name="marks">
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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232 <param name="label" value="H3K4me1" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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233 <param name="reads" value="chr1_h1hesc_h3k4me1.bam" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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234 <param name="mapq" value="0"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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235 <param name="pairedend" value="--pairedend FALSE"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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236 <param name="shift" value="75"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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237 </repeat>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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238 <repeat name="marks">
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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239 <param name="label" value="H4K27me3" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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240 <param name="reads" value="chr1_h1hesc_h3k27me3.bam" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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diff changeset
241 <param name="mapq" value="0"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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242 <param name="pairedend" value="--pairedend FALSE"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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243 <param name="shift" value="75"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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diff changeset
244 </repeat>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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245 </repeat>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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246 <repeat name="datasets">
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247 <param name="name" value="DS2" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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248 <repeat name="marks">
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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249 <param name="label" value="H3K4me3" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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250 <param name="reads" value="chr1_h1hesc_h3k4me3.bam" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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251 <param name="mapq" value="0"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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252 <param name="pairedend" value="--pairedend FALSE"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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253 <param name="shift" value="75"/>
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254 </repeat>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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255 <repeat name="marks">
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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256 <param name="label" value="H3K4me1" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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257 <param name="reads" value="chr1_h1hesc_h3k4me1_rep2.bam" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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258 <param name="mapq" value="0"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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259 <param name="pairedend" value="--pairedend FALSE"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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260 <param name="shift" value="75"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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261 </repeat>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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262 <repeat name="marks">
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263 <param name="label" value="H4K27me3" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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264 <param name="reads" value="chr1_h1hesc_h3k27me3.bam" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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265 <param name="mapq" value="0"/>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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266 <param name="pairedend" value="--pairedend FALSE"/>
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267 <param name="shift" value="75"/>
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268 </repeat>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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269 </repeat>
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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270 <param name="binsize" value="200" />
6260e42c7d49 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/epicseg commit 560df98ab92af885e9d2e909ee8709885e52cbd3
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271 <param name="nstates" value="5" />
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272 <output name="report" file="report_2ds.html"/>
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273 </test>
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274
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275 <test>
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276 <!-- 2 Datasets with annotation -->
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277 <param name="regions" value="chr1.bed"/>
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278 <repeat name="datasets">
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279 <param name="name" value="DS1" />
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280 <repeat name="marks">
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281 <param name="label" value="H3K4me3" />
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282 <param name="reads" value="chr1_h1hesc_h3k4me3.bam" />
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283 <param name="mapq" value="0"/>
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284 <param name="pairedend" value="--pairedend FALSE"/>
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285 <param name="shift" value="75"/>
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286 </repeat>
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287 <repeat name="marks">
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288 <param name="label" value="H3K4me1" />
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289 <param name="reads" value="chr1_h1hesc_h3k4me1.bam" />
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290 <param name="mapq" value="0"/>
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291 <param name="pairedend" value="--pairedend FALSE"/>
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292 <param name="shift" value="75"/>
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293 </repeat>
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294 <repeat name="marks">
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295 <param name="label" value="H4K27me3" />
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296 <param name="reads" value="chr1_h1hesc_h3k27me3.bam" />
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297 <param name="mapq" value="0"/>
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298 <param name="pairedend" value="--pairedend FALSE"/>
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299 <param name="shift" value="75"/>
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300 </repeat>
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301 </repeat>
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302 <repeat name="datasets">
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303 <param name="name" value="DS2" />
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304 <repeat name="marks">
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305 <param name="label" value="H3K4me3" />
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306 <param name="reads" value="chr1_h1hesc_h3k4me3.bam" />
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307 <param name="mapq" value="0"/>
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308 <param name="pairedend" value="--pairedend FALSE"/>
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309 <param name="shift" value="75"/>
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310 </repeat>
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311 <repeat name="marks">
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312 <param name="label" value="H3K4me1" />
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313 <param name="reads" value="chr1_h1hesc_h3k4me1_rep2.bam" />
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314 <param name="mapq" value="0"/>
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315 <param name="pairedend" value="--pairedend FALSE"/>
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316 <param name="shift" value="75"/>
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317 </repeat>
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318 <repeat name="marks">
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319 <param name="label" value="H4K27me3" />
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320 <param name="reads" value="chr1_h1hesc_h3k27me3.bam" />
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321 <param name="mapq" value="0"/>
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322 <param name="pairedend" value="--pairedend FALSE"/>
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323 <param name="shift" value="75"/>
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324 </repeat>
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325 </repeat>
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326 <param name="binsize" value="200" />
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327 <param name="nstates" value="5" />
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328 <repeat name="annots">
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329 <param name="name" value="cpg" />
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330 <param name="file" value="cpgIslandExt.hg19.bed" />
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331 </repeat>
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332 <output name="report" file="report_2ds_w_annot.html"/>
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333 </test>
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334 </tests>
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335 <help><![CDATA[
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336 .. class:: infomark
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337
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338 **What it does**
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339
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340 **EpiCSeg - Chromatin segmentation** is a tool for performing chromatin segmentation.
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341 It takes as input
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342
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343 1. one or more datasets (e.g. cell-types or conditions)
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344 which consist of the next-generation sequencing alignments
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345 (in bam format) for a common set of chromatin marks (e.g. H3K27me3, H3K4me3, etc.)
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346 2. a bed file containing the regions of interest
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347 3. (optional) a set of annotation files (in bed format)
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348 against which the segmentation results are compared.
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349 For example, CpG island annotation.
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350
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351 It produces
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352
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353 1. an html report that summarizes the chromatin segmentation results
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354 2. a bed file per dataset that contains the chromatin segments.
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355
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356 ]]></help>
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357 <expand macro="citations" />
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358 </tool>