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annotate unionBedGraphs.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 7a06bb42dbb1
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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_unionbedgraph" name="bedtools Merge BedGraph files" version="@TOOL_VERSION@">
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2 <description>combines coverage intervals from multiple BEDGRAPH 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 unionBedGraphs
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10 $header
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11 -filler '${filler}'
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12 $empty.empty_selector
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13 @GENOME_FILE_UNION@
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14
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15 #if str($tag.tag_select) == "tag":
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16 -i
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17 #for $file in $tag.inputs:
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18 '${file}'
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19 #end for
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20 #else:
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21 -i
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22 #for $bg in $tag.bedgraphs:
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23 '${bg.input}'
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24 #end for
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25 -names
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26 #for $bg in $tag.bedgraphs:
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27 '${bg.custom_name}'
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28 #end for
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29 #end if
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30 > '${output}'
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31 ]]></command>
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32 <inputs>
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33 <conditional name="tag">
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34 <param name="tag_select" type="select" label="Sample name">
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35 <option value="tag" selected="true">Use input's tag</option>
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36 <option value="custom">Enter custom name per file</option>
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37 </param>
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38 <when value="tag">
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39 <param name="inputs" argument="-i" type="data" format="bedgraph" multiple="true" label="BedGraph files" />
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40 </when>
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41 <when value="custom">
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42 <repeat name="bedgraphs" title="Add BedGraph files" min="2">
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43 <param name="input" argument="-i" type="data" format="bedgraph" multiple="true" label="BedGraph file" />
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44 <param name="custom_name" argument="-names" type="text" area="false" label="Custom sample name" />
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45 </repeat>
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46 </when>
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47 </conditional>
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48 <conditional name="empty">
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49 <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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50 <option value="-empty">Yes</option>
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51 <option value="">No</option>
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52 </param>
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53 <when value="-empty">
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54 <expand macro="input_conditional_genome_file" />
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55 </when>
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56 <when value="" />
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57 </conditional>
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58 <param argument="-filler" type="text" value="N/A"
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59 label="Text to use for no-coverage value"
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60 help="Can be 0.0, N/A, - or any other value" />
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61 <expand macro="print_header" />
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62 </inputs>
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63 <outputs>
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64 <data name="output" format="bedgraph" />
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65 </outputs>
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66 <tests>
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67 <test>
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68 <param name="tag_select" value="tag" />
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69 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
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70 <param name="empty_selector" value="" />
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71 <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" />
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72 </test>
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73 <test>
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74 <param name="tag_select" value="tag" />
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75 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
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76 <param name="header" value="True" />
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77 <param name="empty_selector" value="" />
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78 <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" />
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79 </test>
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80 <test>
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81 <param name="tag_select" value="tag" />
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82 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
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83 <param name="empty_selector" value="-empty" />
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84 <param name="genome_file_opts_selector" value="hist" />
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85 <param name="genome" value="unionBedGraphs1.len" />
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86 <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" />
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87 </test>
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88 <test>
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89 <param name="tag_select" value="custom" />
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90 <repeat name="bedgraphs">
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91 <param name="input" value="unionBedGraphs1.bg" />
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92 <param name="custom_name" value="first" />
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93 </repeat>
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94 <repeat name="bedgraphs">
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95 <param name="input" value="unionBedGraphs2.bg" />
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96 <param name="custom_name" value="second" />
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97 </repeat>
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98 <repeat name="bedgraphs">
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99 <param name="input" value="unionBedGraphs3.bg" />
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100 <param name="custom_name" value="third" />
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101 </repeat>
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102 <param name="empty_selector" value="-empty" />
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103 <param name="genome_file_opts_selector" value="hist" />
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104 <param name="genome" value="unionBedGraphs1.len" />
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105 <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
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106 </test>
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107 </tests>
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108 <help><![CDATA[
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109 **What it does**
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110
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111 This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.
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112
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113 .. class:: warningmark
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114
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115 This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file).
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116
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118 ------
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119
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120 **Example input**::
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121
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122 # 1.bedgraph
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123 chr1 1000 1500 10
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124 chr1 2000 2100 20
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125
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126 # 2.bedgraph
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127 chr1 900 1600 60
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128 chr1 1700 2050 50
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129
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130 # 3.bedgraph
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131 chr1 1980 2070 80
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132 chr1 2090 2100 20
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133
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134
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135 ------
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136
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137 **Examples using the Zero Coverage checkbox**
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parents:
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138
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parents:
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139 Output example (*without* checking "Report regions with zero coverage")::
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parents: 17
diff changeset
140
8
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iuc
parents:
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141 chr1 900 1000 0 60 0
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iuc
parents:
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142 chr1 1000 1500 10 60 0
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iuc
parents:
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143 chr1 1500 1600 0 60 0
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iuc
parents:
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144 chr1 1700 1980 0 50 0
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iuc
parents:
diff changeset
145 chr1 1980 2000 0 50 80
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iuc
parents:
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146 chr1 2000 2050 20 50 80
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iuc
parents:
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147 chr1 2050 2070 20 0 80
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iuc
parents:
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148 chr1 2070 2090 20 0 0
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iuc
parents:
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149 chr1 2090 2100 20 0 20
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iuc
parents:
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150
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parents:
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151
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parents:
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152 Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).::
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parents: 17
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153
8
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iuc
parents:
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154 chr1 0 900 0 0 0 (*)
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iuc
parents:
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155 chr1 900 1000 0 60 0
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iuc
parents:
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156 chr1 1000 1500 10 60 0
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iuc
parents:
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157 chr1 1500 1600 0 60 0
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iuc
parents:
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158 chr1 1600 1700 0 0 0 (*)
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iuc
parents:
diff changeset
159 chr1 1700 1980 0 50 0
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iuc
parents:
diff changeset
160 chr1 1980 2000 0 50 80
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iuc
parents:
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161 chr1 2000 2050 20 50 80
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iuc
parents:
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162 chr1 2050 2070 20 0 80
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iuc
parents:
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163 chr1 2070 2090 20 0 0
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iuc
parents:
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164 chr1 2090 2100 20 0 20
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iuc
parents: 17
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165 chr1 2100 247249719 0 0 0 (*)
8
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iuc
parents:
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166
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iuc
parents:
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167
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iuc
parents:
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168 ------
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iuc
parents:
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169
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iuc
parents:
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170 **Examples adjusting the "Filler value" for no-covered intervals**
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parents:
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171
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parents:
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172 The default value is '0', but you can use any other value.
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parents:
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173
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parents:
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174 Output example with **filler = N/A**::
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iuc
parents: 17
diff changeset
175
8
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iuc
parents:
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176 chr1 900 1000 N/A 60 N/A
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iuc
parents:
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177 chr1 1000 1500 10 60 N/A
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iuc
parents:
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178 chr1 1500 1600 N/A 60 N/A
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iuc
parents:
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179 chr1 1600 1700 N/A N/A N/A
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iuc
parents:
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180 chr1 1700 1980 N/A 50 N/A
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iuc
parents:
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181 chr1 1980 2000 N/A 50 80
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iuc
parents:
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182 chr1 2000 2050 20 50 80
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iuc
parents:
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183 chr1 2050 2070 20 N/A 80
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iuc
parents:
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184 chr1 2070 2090 20 N/A N/A
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iuc
parents:
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185 chr1 2090 2100 20 N/A 20
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iuc
parents:
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186
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iuc
parents:
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187
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iuc
parents:
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188 ------
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iuc
parents:
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189
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parents:
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190 **Examples using the "sample name" labels**::
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iuc
parents:
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191
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iuc
parents:
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192 chrom start end WT-1 WT-2 KO-1
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iuc
parents:
diff changeset
193 chr1 900 1000 N/A 60 N/A
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iuc
parents:
diff changeset
194 chr1 1000 1500 10 60 N/A
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iuc
parents:
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195 chr1 1500 1600 N/A 60 N/A
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iuc
parents:
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196 chr1 1600 1700 N/A N/A N/A
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iuc
parents:
diff changeset
197 chr1 1700 1980 N/A 50 N/A
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iuc
parents:
diff changeset
198 chr1 1980 2000 N/A 50 80
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iuc
parents:
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199 chr1 2000 2050 20 50 80
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iuc
parents:
diff changeset
200 chr1 2050 2070 20 N/A 80
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iuc
parents:
diff changeset
201 chr1 2070 2090 20 N/A N/A
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iuc
parents:
diff changeset
202 chr1 2090 2100 20 N/A 20
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iuc
parents:
diff changeset
203
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iuc
parents:
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204
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iuc
parents:
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205 ------
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iuc
parents:
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206
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parents:
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207 **Non-numeric values**
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parents:
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208
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iuc
parents:
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209 The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value.
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parents:
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210
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parents:
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211 Input Example::
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iuc
parents: 17
diff changeset
212
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
213 File-1 File-2
8
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iuc
parents:
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214 chr1 200 300 Sample1 chr1 100 240 0.75
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iuc
parents:
diff changeset
215 chr1 400 450 Sample1 chr1 250 700 0.43
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iuc
parents:
diff changeset
216 chr1 530 600 Sample2
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iuc
parents:
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217
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iuc
parents:
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218 Output Example::
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iuc
parents: 17
diff changeset
219
8
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iuc
parents:
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220 chr1 100 200 0 0.75
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iuc
parents:
diff changeset
221 chr1 200 240 Sample1 0.75
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iuc
parents:
diff changeset
222 chr1 240 250 Sample1 0
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iuc
parents:
diff changeset
223 chr1 250 300 Sample1 0.43
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iuc
parents:
diff changeset
224 chr1 300 400 0 0.43
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iuc
parents:
diff changeset
225 chr1 400 450 Sample1 0.43
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iuc
parents:
diff changeset
226 chr1 450 530 0 0.43
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iuc
parents:
diff changeset
227 chr1 530 600 Sample2 0.43
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iuc
parents:
diff changeset
228 chr1 600 700 0 0.43
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iuc
parents:
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229
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iuc
parents:
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230 @REFERENCES@
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iuc
parents: 48
diff changeset
231 ]]></help>
8
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iuc
parents:
diff changeset
232 <expand macro="citations" />
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iuc
parents:
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233 </tool>