bedtools: unionBedGraphs.xml annotate

annotate unionBedGraphs.xml @ 46:64e2edfe7a2c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4

author	iuc
date	Sat, 18 May 2024 23:28:38 +0000
parents	7ab85ac5f64b
children

rev	line source
39 3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2" iuc parents: 34 diff changeset	1 <tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@TOOL_VERSION@" profile="@PROFILE@">
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	2 <description>combines coverage intervals from multiple BEDGRAPH files</description>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	3 <macros>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	4 <import>macros.xml</import>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	5 </macros>
41 7ab85ac5f64b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b" iuc parents: 39 diff changeset	6 <expand macro="bio_tools" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	7 <expand macro="requirements" />
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	8 <expand macro="stdio" />
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	9 <command><![CDATA[
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	10 unionBedGraphs
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	11 $header
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	12 -filler '${filler}'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	13 $empty.empty_selector
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	14 @GENOME_FILE_UNION@
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	15
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	16 #if str($tag.tag_select) == "tag":
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	17 -i
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	18 #for $file in $tag.inputs:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	19 '${file}'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	20 #end for
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	21 #else:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	22 -i
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	23 #for $bg in $tag.bedgraphs:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	24 '${bg.input}'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	25 #end for
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	26 -names
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	27 #for $bg in $tag.bedgraphs:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	28 '${bg.custom_name}'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	29 #end for
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	30 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	31 > '${output}'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	32 ]]></command>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	33 <inputs>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	34 <conditional name="tag">
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	35 <param name="tag_select" type="select" label="Sample name">
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	36 <option value="tag" selected="true">Use input's tag</option>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	37 <option value="custom">Enter custom name per file</option>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	38 </param>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	39 <when value="tag">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	40 <param name="inputs" argument="-i" type="data" format="bedgraph" multiple="true" label="BedGraph files" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	41 </when>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	42 <when value="custom">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	43 <repeat name="bedgraphs" title="Add BedGraph files" min="2">
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	44 <param name="input" argument="-i" type="data" format="bedgraph" multiple="true" label="BedGraph file" />
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	45 <param name="custom_name" argument="-names" type="text" area="false" label="Custom sample name" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	46 </repeat>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	47 </when>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	48 </conditional>
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	49 <conditional name="empty">
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	50 <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	51 <option value="-empty">Yes</option>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	52 <option value="">No</option>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	53 </param>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	54 <when value="-empty">
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	55 <expand macro="input_conditional_genome_file" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	56 </when>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	57 <when value="" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	58 </conditional>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	59 <param argument="-filler" type="text" value="N/A"
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	60 label="Text to use for no-coverage value"
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	61 help="Can be 0.0, N/A, - or any other value" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	62 <expand macro="print_header" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	63 </inputs>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	64 <outputs>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	65 <data name="output" format="bedgraph" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	66 </outputs>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	67 <tests>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	68 <test>
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	69 <param name="tag_select" value="tag" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	70 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	71 <param name="empty_selector" value="" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	72 <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	73 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	74 <test>
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	75 <param name="tag_select" value="tag" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	76 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	77 <param name="header" value="True" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	78 <param name="empty_selector" value="" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	79 <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	80 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	81 <test>
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	82 <param name="tag_select" value="tag" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	83 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	84 <param name="empty_selector" value="-empty" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	85 <param name="genome_file_opts_selector" value="hist" />
41 7ab85ac5f64b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b" iuc parents: 39 diff changeset	86 <param name="genome" value="unionBedGraphs1.len" ftype="tabular" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	87 <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	88 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	89 <test>
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	90 <param name="tag_select" value="custom" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	91 <repeat name="bedgraphs">
41 7ab85ac5f64b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b" iuc parents: 39 diff changeset	92 <param name="input" value="unionBedGraphs1.bg" ftype="bedgraph" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	93 <param name="custom_name" value="first" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	94 </repeat>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	95 <repeat name="bedgraphs">
41 7ab85ac5f64b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b" iuc parents: 39 diff changeset	96 <param name="input" value="unionBedGraphs2.bg" ftype="bedgraph" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	97 <param name="custom_name" value="second" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	98 </repeat>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	99 <repeat name="bedgraphs">
41 7ab85ac5f64b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b" iuc parents: 39 diff changeset	100 <param name="input" value="unionBedGraphs3.bg" ftype="bedgraph" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	101 <param name="custom_name" value="third" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	102 </repeat>
17 44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	103 <param name="empty_selector" value="-empty" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174 iuc parents: 11 diff changeset	104 <param name="genome_file_opts_selector" value="hist" />
41 7ab85ac5f64b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b" iuc parents: 39 diff changeset	105 <param name="genome" value="unionBedGraphs1.len" ftype="tabular" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	106 <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	107 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	108 </tests>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	109 <help><![CDATA[
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	110 What it does
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	111
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	112 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.
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	113
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	114 .. class:: warningmark
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	115
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	116 This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file).
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	117
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	118
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	119 ------
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	120
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	121 Example input::
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	122
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	123 # 1.bedgraph
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	124 chr1 1000 1500 10
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	125 chr1 2000 2100 20
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	126
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	127 # 2.bedgraph
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	128 chr1 900 1600 60
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	129 chr1 1700 2050 50
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	130
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	131 # 3.bedgraph
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	132 chr1 1980 2070 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	133 chr1 2090 2100 20
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	134
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	135
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	136 ------
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	137
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	138 Examples using the Zero Coverage checkbox
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	139
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	140 Output example (without checking "Report regions with zero coverage")::
11 7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811 iuc parents: 10 diff changeset	141
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	142 chr1 900 1000 0 60 0
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	143 chr1 1000 1500 10 60 0
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	144 chr1 1500 1600 0 60 0
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	145 chr1 1700 1980 0 50 0
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	146 chr1 1980 2000 0 50 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	147 chr1 2000 2050 20 50 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	148 chr1 2050 2070 20 0 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	149 chr1 2070 2090 20 0 0
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	150 chr1 2090 2100 20 0 20
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	151
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	152
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	153 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).::
11 7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811 iuc parents: 10 diff changeset	154
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	155 chr1 0 900 0 0 0 (*)
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	156 chr1 900 1000 0 60 0
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	157 chr1 1000 1500 10 60 0
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	158 chr1 1500 1600 0 60 0
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	159 chr1 1600 1700 0 0 0 (*)
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	160 chr1 1700 1980 0 50 0
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	161 chr1 1980 2000 0 50 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	162 chr1 2000 2050 20 50 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	163 chr1 2050 2070 20 0 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	164 chr1 2070 2090 20 0 0
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	165 chr1 2090 2100 20 0 20
11 7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811 iuc parents: 10 diff changeset	166 chr1 2100 247249719 0 0 0 (*)
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	167
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	168
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	169 ------
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	170
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	171 Examples adjusting the "Filler value" for no-covered intervals
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	172
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	173 The default value is '0', but you can use any other value.
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	174
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	175 Output example with filler = N/A::
11 7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811 iuc parents: 10 diff changeset	176
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	177 chr1 900 1000 N/A 60 N/A
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	178 chr1 1000 1500 10 60 N/A
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	179 chr1 1500 1600 N/A 60 N/A
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	180 chr1 1600 1700 N/A N/A N/A
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	181 chr1 1700 1980 N/A 50 N/A
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	182 chr1 1980 2000 N/A 50 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	183 chr1 2000 2050 20 50 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	184 chr1 2050 2070 20 N/A 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	185 chr1 2070 2090 20 N/A N/A
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	186 chr1 2090 2100 20 N/A 20
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	187
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	188
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	189 ------
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	190
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	191 Examples using the "sample name" labels::
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	192
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	193 chrom start end WT-1 WT-2 KO-1
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	194 chr1 900 1000 N/A 60 N/A
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	195 chr1 1000 1500 10 60 N/A
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	196 chr1 1500 1600 N/A 60 N/A
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	197 chr1 1600 1700 N/A N/A N/A
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	198 chr1 1700 1980 N/A 50 N/A
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	199 chr1 1980 2000 N/A 50 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	200 chr1 2000 2050 20 50 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	201 chr1 2050 2070 20 N/A 80
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	202 chr1 2070 2090 20 N/A N/A
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	203 chr1 2090 2100 20 N/A 20
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	204
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	205
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	206 ------
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	207
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	208 Non-numeric values
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	209
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	210 The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value.
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	211
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	212 Input Example::
11 7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811 iuc parents: 10 diff changeset	213
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811 iuc parents: 10 diff changeset	214 File-1 File-2
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	215 chr1 200 300 Sample1 chr1 100 240 0.75
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	216 chr1 400 450 Sample1 chr1 250 700 0.43
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	217 chr1 530 600 Sample2
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	218
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	219 Output Example::
11 7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811 iuc parents: 10 diff changeset	220
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	221 chr1 100 200 0 0.75
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	222 chr1 200 240 Sample1 0.75
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	223 chr1 240 250 Sample1 0
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	224 chr1 250 300 Sample1 0.43
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	225 chr1 300 400 0 0.43
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	226 chr1 400 450 Sample1 0.43
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	227 chr1 450 530 0 0.43
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	228 chr1 530 600 Sample2 0.43
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	229 chr1 600 700 0 0.43
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	230
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	231 @REFERENCES@
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	232 ]]></help>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	233 <expand macro="citations" />
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	234 </tool>

Mercurial > repos > iuc > bedtools

annotate unionBedGraphs.xml @ 46:64e2edfe7a2c draft default tip