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annotate multiIntersectBed.xml @ 50:df28283b3778 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:54:22 -0400
parents 2f457890d8c8
children 9a9f1a7abf54
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50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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1 <tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@+galaxy1">
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2 <description>identifies common intervals among multiple interval files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command><![CDATA[
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9 bedtools multiinter
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10 $header
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11 $cluster
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12 -filler '${filler}'
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13 $empty.empty_selector
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14 @GENOME_FILE_UNION@
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15
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16 #if str($tag.tag_select) == "tag":
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17 -i
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18 #for $file in $tag.inputs
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19 '$file'
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20 #end for
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21 #else:
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22 -i
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23 #for $file in $tag.beds:
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24 '${file.input}'
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25 #end for
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26 -names
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27 #for $file in $tag.beds:
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28 '{$file.custom_name}'
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29 #end for
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30 #end if
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31 > '$output'
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32 ]]></command>
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33 <inputs>
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34 <conditional name="tag">
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35 <param name="tag_select" type="select" label="Sample name">
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36 <option value="tag" selected="true">Use input's tag</option>
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37 <option value="custom">Enter custom name per file</option>
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38 </param>
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39 <when value="tag">
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40 <param name="inputs" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
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41 </when>
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42 <when value="custom">
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43 <repeat name="beds" title="Add BED files" min="2" >
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44 <param name="input" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
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45 <param name="custom_name" type="text" area="false" label="Custom sample name" />
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46 </repeat>
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47 </when>
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48 </conditional>
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49 <param argument="-cluster" type="boolean" truevalue="-cluster" falsevalue="" checked="false"
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50 label="Invoke Ryan Layers's clustering algorithm" />
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51 <conditional name="empty">
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52 <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">
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53 <option value="-empty">Yes</option>
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54 <option value="">No</option>
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55 </param>
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56 <when value="-empty">
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57 <expand macro="input_conditional_genome_file" />
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58 </when>
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59 <when value="" />
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60 </conditional>
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61 <param argument="-filler" type="text" value="N/A"
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62 label="Text to use for no-coverage value"
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63 help="Can be 0.0, N/A, - or any other value" />
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64 <expand macro="print_header" />
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65 </inputs>
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66 <outputs>
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67 <data name="output" format="bed" />
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="tag_select" value="tag" />
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72 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
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73 <param name="empty_selector" value="" />
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74 <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" />
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75 </test>
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76 <test>
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77 <param name="tag_select" value="tag" />
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78 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
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79 <param name="header" value="True" />
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80 <param name="empty_selector" value="" />
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81 <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" />
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82 </test>
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83 <test>
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84 <param name="tag_select" value="tag" />
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85 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
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86 <param name="empty_selector" value="-empty" />
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87 <param name="genome_file_opts_selector" value="hist" />
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88 <param name="genome" value="multiIntersectBed1.len" />
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89 <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
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90 </test>
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91 </tests>
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92 <help><![CDATA[
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93 **What it does**
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94
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95 This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files.
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96
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97
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98 .. class:: warningmark
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99
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100 This tool requires that each BED file is reference-sorted (chrom, then start).
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101
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102
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103 .. class:: infomark
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104
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105 The output file will contain five fixed columns, plus additional columns for each BED file:
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106
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107 * 1. Chromosome name (or 'genome' for whole-genome coverage).
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108 * 2. The zero-based start position of the interval.
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109 * 3. The one-based end position of the interval.
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110 * 4. The number of input files that had at least one feature overlapping this interval.
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111 * 5. A list of input files or labels that had at least one feature overlapping this interval.
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112 * 6. For each input file, an indication (1 = Yes, 0 = No) of whether or not the file had at least one feature overlapping this interval.
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113
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114 ------
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115
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116 **Example input**::
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117
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118 # a.bed
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119 chr1 6 12bed
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120 chr1 10 20
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121 chr1 22 27
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122 chr1 24 30
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123
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124 # b.bed
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125 chr1 12 32
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126 chr1 14 30
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127
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128 # c.bed
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129 chr1 8 15
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130 chr1 10 14
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131 chr1 32 34
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132
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133
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134 ------
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135
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136 **Example without a header and without reporting intervals with zero coverage**::
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137
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138
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parents:
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139 chr1 6 8 1 1 1 0 0
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iuc
parents:
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140 chr1 8 12 2 1,3 1 0 1
0d3aa592ce27 Uploaded
iuc
parents:
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141 chr1 12 15 3 1,2,3 1 1 1
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iuc
parents:
diff changeset
142 chr1 15 20 2 1,2 1 1 0
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
143 chr1 20 22 1 2 0 1 0
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
144 chr1 22 30 2 1,2 1 1 0
0d3aa592ce27 Uploaded
iuc
parents:
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145 chr1 30 32 1 2 0 1 0
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iuc
parents:
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146 chr1 32 34 1 3 0 0 1
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iuc
parents:
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147
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iuc
parents:
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148
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iuc
parents:
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149 **Example adding a header line**::
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iuc
parents:
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150
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iuc
parents:
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151
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iuc
parents:
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152 chrom start end num list a.bed b.bed c.bed
0d3aa592ce27 Uploaded
iuc
parents:
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153 chr1 6 8 1 1 1 0 0
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iuc
parents:
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154 chr1 8 12 2 1,3 1 0 1
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
155 chr1 12 15 3 1,2,3 1 1 1
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iuc
parents:
diff changeset
156 chr1 15 20 2 1,2 1 1 0
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iuc
parents:
diff changeset
157 chr1 20 22 1 2 0 1 0
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iuc
parents:
diff changeset
158 chr1 22 30 2 1,2 1 1 0
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iuc
parents:
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159 chr1 30 32 1 2 0 1 0
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iuc
parents:
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160 chr1 32 34 1 3 0 0 1
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iuc
parents:
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161
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iuc
parents:
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162
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iuc
parents:
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163 **Example adding a header line and custom file labels**::
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iuc
parents:
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164
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iuc
parents:
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165
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iuc
parents:
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166 chrom start end num list joe bob sue
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iuc
parents:
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167 chr1 6 8 1 joe 1 0 0
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iuc
parents:
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168 chr1 8 12 2 joe,sue 1 0 1
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iuc
parents:
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169 chr1 12 15 3 joe,bob,sue 1 1 1
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iuc
parents:
diff changeset
170 chr1 15 20 2 joe,bob 1 1 0
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iuc
parents:
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171 chr1 20 22 1 bob 0 1 0
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iuc
parents:
diff changeset
172 chr1 22 30 2 joe,bob 1 1 0
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iuc
parents:
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173 chr1 30 32 1 bob 0 1 0
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iuc
parents:
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174 chr1 32 34 1 sue 0 0 1
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iuc
parents:
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175
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iuc
parents:
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176
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iuc
parents:
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177 @REFERENCES@
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
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178 ]]></help>
8
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iuc
parents:
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179 <expand macro="citations" />
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iuc
parents:
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180 </tool>