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1 <tool id="ideas_preprocessor" name="IDEAS preprocessor" version="1.0.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="2.5.4">deeptools</requirement>
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5 <requirement type="package" version="1.10.4">r-data.table</requirement>
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6 <requirement type="package" version="1.4.4">r-optparse</requirement>
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7 <requirement type="package" version="1.6">samtools</requirement>
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8 <requirement type="package" version="357">ucsc-bigwigaverageoverbed</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #set tmp_dir = "tmp"
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12 #set prep_input_config = "prep_input_config.txt"
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13 #set prep_output_config = "prep_output_config.txt"
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14 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
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2
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15 mkdir $tmp_dir &&
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16 mkdir $output.files_path &&
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17 #if str($specify_genomic_window) == "yes":
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18 ##############################################
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19 ## Using a genomic window bed file, so categorize
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20 ## the window positions by chromosome to enable
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21 ## the IDEAS -inv option.
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22 ##############################################
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23 #set windows_positions_by_chroms_config = "windows_positions_by_chroms_config.txt"
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24 cp '$gen_windows_positions_by_chroms_config' $windows_positions_by_chroms_config &&
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25 #end if
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0
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26 ##############################################
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27 ## Create the config file and prepare the data
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28 ##############################################
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29 cp '$gen_prep_input_config' $prep_input_config &&
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30 sort $prep_input_config -o $prep_input_config &&
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31 Rscript '$__tool_directory__/ideas_preprocessor.R'
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32 --prep_input_config '$prep_input_config'
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33 #if str($specify_genomic_window) == "yes":
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2
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34 --prep_output_config '$prep_output_config'
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35 --windows_positions_by_chroms_config '$windows_positions_by_chroms_config'
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36 #end if
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37 #if str($specify_genomic_window) == "yes":
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38 --bed_input '$specify_genomic_window_cond.bed_input'
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39 #else:
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40 --chrom_len_file '$chromInfo'
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41 --window_size $specify_genomic_window_cond.window_size
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42 #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes
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43 #if str($restrict_chromosomes) == "yes":
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44 #set chroms = []
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45 #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat
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46 #for $i in $chrom_repeat.chrom
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47 $chroms.append($i)
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48 #end for
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49 --restrict_to_chroms ",".join(chroms)
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50 #end if
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51 #end if
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52 --reads_per_bp $reads_per_bp
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2
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53 #if str($exclude_input) not in ["None", ""]:
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54 --exclude_input '$exclude_input'
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55 #end if
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56 --output '$output'
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57 --output_files_path '$output.files_path'
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58 &> ideas_preprocessor_log.txt;
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59 if [[ $? -ne 0 ]]; then
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60 cp ideas_preprocessor_log.txt '$output';
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61 exit 1;
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62 fi
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63 ]]></command>
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64 <configfiles>
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65 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
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66 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
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67 #for $i in $cell_type_epigenetic_factor_cond.input:
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68 #set file_name_with_ext = $i.name
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69 #if str($file_name_with_ext).find("http") >= 0 or str($file_name_with_ext).find("ftp") >= 0:
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70 #set file_name_with_ext = $file_name_with_ext.split('/')[-1]
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71 #end if
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72 #assert str($file_name_with_ext).find("-") >= 0, "The selected input '%s' is invalid because it does not include the '-' character which is required when setting cell type and epigenetic factor names by extracting them from the input file names." % $file_name_with_ext
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73 #set file_name = $file_name_with_ext.split(".")[0]
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74 #if str($input_name_positions) == "cell_first":
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75 #set cell_type_name = $file_name.split("-")[0]
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76 #set epigenetic_factor_name = $file_name.split("-")[1]
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77 #else:
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78 #set cell_type_name = $file_name.split("-")[1]
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79 #set epigenetic_factor_name = $file_name.split("-")[0]
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80 #end if
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81 ${cell_type_name} ${epigenetic_factor_name} ${i} ${file_name} ${i.ext}
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0
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82 #end for
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83 #else:
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84 #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat:
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85 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} ${file_name} ${input_items.input.ext}
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86 #end for
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87 #end if]]></configfile>
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88 <configfile name="gen_windows_positions_by_chroms_config"><![CDATA[#if str($specify_genomic_window_cond.specify_genomic_window) == "yes":
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89 #import collections
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90 #set window_positions_by_chroms_odict = $collections.OrderedDict()
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91 #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')):
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92 #set $line = $line.strip()
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93 #if not $line or $line.startswith('#'):
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94 #continue
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95 #end if
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96 #set items = $line.split('\t')
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97 #if $items[0] in $window_positions_by_chroms_odict:
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98 #set tup = $window_positions_by_chroms_odict[$items[0]]
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99 #set $tup[1] += 1
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100 #set $window_positions_by_chroms_odict[$items[0]] = $tup
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101 #else:
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102 #set $window_positions_by_chroms_odict[$items[0]] = [$count, $count+1]
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103 #end if
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104 #end for
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105 #for $chrom, $tup in $window_positions_by_chroms_odict.items():
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106 ${chrom} ${tup[0]} ${tup[1]}
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107 #end for
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108 #end if]]></configfile>
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109 </configfiles>
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110 <inputs>
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111 <conditional name="cell_type_epigenetic_factor_cond">
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112 <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by">
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113 <option value="extract" selected="true">extracting them from the selected input file names</option>
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114 <option value="manual">manually setting them for each selected input</option>
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115 </param>
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116 <when value="extract">
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117 <param name="input" type="data" format="bigwig,bam" multiple="True" label="BAM or BigWig files">
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118 <validator type="empty_field"/>
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119 <validator type="unspecified_build"/>
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120 </param>
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121 <param name="input_name_positions" type="select" display="radio" label="Selected input file name pattern is" help="A '-' character must separate cell type and epigenetic factor names within the selected input file names">
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122 <option value="cell_first" selected="true">Cell type name - Epigenetic factor name</option>
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123 <option value="cell_last">Epigenetic factor name - Cell type name</option>
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124 </param>
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125 </when>
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126 <when value="manual">
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127 <repeat name="input_repeat" title="Cell type, Epigenetic factor and Input" min="1">
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128 <param name="cell_type_name" type="text" value="" label="Cell type name">
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129 <validator type="empty_field"/>
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130 </param>
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131 <param name="epigenetic_factor_name" type="text" value="" label="Epigenetic factor name">
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132 <validator type="empty_field"/>
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133 </param>
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134 <param name="input" type="data" format="bigwig,bam" label="BAM or BigWig file">
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135 <validator type="empty_field"/>
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136 <validator type="unspecified_build"/>
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137 </param>
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138 </repeat>
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139 </when>
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140 </conditional>
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141 <conditional name="specify_genomic_window_cond">
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142 <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data">
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143 <option value="no" selected="true">No</option>
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144 <option value="yes">Yes</option>
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145 </param>
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146 <when value="no">
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147 <param name="window_size" type="integer" value="200" label="Window size in base pairs"/>
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148 <conditional name="restrict_chromosomes_cond">
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149 <param name="restrict_chromosomes" type="select" label="Restrict processing to specified chromosomes">
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150 <option value="no" selected="true">No</option>
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151 <option value="yes">Yes</option>
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152 </param>
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153 <when value="no"/>
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154 <when value="yes">
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155 <repeat name="chrom_repeat" title="Chromosomes" min="1">
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156 <param name="chrom" type="text" value="" label="Chromosome" help="One chromosome (e.g., chr1, chr2, chrX) per text field"/>
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157 </repeat>
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158 </when>
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159 </conditional>
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160 </when>
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161 <when value="yes">
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162 <param name="bed_input" type="data" format="bed" label="Bed file specifying the genomic windows"/>
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163 </when>
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164 </conditional>
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165 <param argument="--bychr" type="boolean" truevalue="true" falsevalue="" checked="False" label="Output chromosomes in separate files"/>
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166 <param name="reads_per_bp" type="select" display="radio" label="Calculate the signal in each genomic window using">
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167 <option value="6" selected="true">mean</option>
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168 <option value="8">max</option>
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169 </param>
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170 <param name="exclude_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/>
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171 <param argument="--standardize_datasets" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/>
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172 </inputs>
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173 <outputs>
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174 <data name="output" format="html"/>
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175 </outputs>
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176 <tests>
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177 <test>
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178 </test>
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179 </tests>
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180 <help>
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181 **What it does**
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182
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183 -----
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184
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185 **Required options**
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186
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187 </help>
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188 <citations>
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189 <citation type="doi">10.1093/nar/gkw278</citation>
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190 </citations>
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191 </tool>
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