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comparison 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
comparison
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49:5074e81a5ce1 50:df28283b3778
1 <tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@TOOL_VERSION@">
2 <description>combines coverage intervals from multiple BEDGRAPH files</description> 2 <description>combines coverage intervals from multiple BEDGRAPH files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command><![CDATA[
9 <![CDATA[ 9 unionBedGraphs
10 unionBedGraphs 10 $header
11 $header 11 -filler '${filler}'
12 -filler "${filler}" 12 $empty.empty_selector
13 $empty.empty_selector 13 @GENOME_FILE_UNION@
14 @GENOME_FILE_UNION@ 14
15 15 #if str($tag.tag_select) == "tag":
16 #if str($tag.tag_select) == "tag": 16 -i
17 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] ) 17 #for $file in $tag.inputs:
18 -i "${files}" 18 '${file}'
19 #else: 19 #end for
20 -i 20 #else:
21 #for $bg in $tag.bedgraphs: 21 -i
22 "${bg.input}" 22 #for $bg in $tag.bedgraphs:
23 #end for 23 '${bg.input}'
24 -names 24 #end for
25 #for $bg in $tag.bedgraphs: 25 -names
26 "${bg.custom_name}" 26 #for $bg in $tag.bedgraphs:
27 #end for 27 '${bg.custom_name}'
28 #end if 28 #end for
29 > "${output}" 29 #end if
30 ]]> 30 > '${output}'
31 </command> 31 ]]></command>
32 <inputs> 32 <inputs>
33 <conditional name="tag"> 33 <conditional name="tag">
34 <param name="tag_select" type="select" label="Sample name"> 34 <param name="tag_select" type="select" label="Sample name">
35 <option value="tag" selected="true">Use input's tag</option> 35 <option value="tag" selected="true">Use input's tag</option>
36 <option value="custom">Enter custom name per file</option> 36 <option value="custom">Enter custom name per file</option>
37 </param> 37 </param>
38 <when value="tag"> 38 <when value="tag">
39 <param name="inputs" format="bedgraph" type="data" multiple="True" label="BedGraph files" /> 39 <param name="inputs" argument="-i" type="data" format="bedgraph" multiple="true" label="BedGraph files" />
40 </when> 40 </when>
41 <when value="custom"> 41 <when value="custom">
42 <repeat name="bedgraphs" title="Add BedGraph files" min="2" > 42 <repeat name="bedgraphs" title="Add BedGraph files" min="2">
43 <param name="input" format="bedgraph" type="data" multiple="True" label="BedGraph file" /> 43 <param name="input" argument="-i" type="data" format="bedgraph" multiple="true" label="BedGraph file" />
44 <param name="custom_name" type="text" area="false" label="Custom sample name" /> 44 <param name="custom_name" argument="-names" type="text" area="false" label="Custom sample name" />
45 </repeat> 45 </repeat>
46 </when> 46 </when>
47 </conditional> 47 </conditional>
48 <conditional name="empty"> 48 <conditional name="empty">
49 <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets"> 49 <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">
53 <when value="-empty"> 53 <when value="-empty">
54 <expand macro="input_conditional_genome_file" /> 54 <expand macro="input_conditional_genome_file" />
55 </when> 55 </when>
56 <when value="" /> 56 <when value="" />
57 </conditional> 57 </conditional>
58 <param name="filler" type="text" value="N/A" 58 <param argument="-filler" type="text" value="N/A"
59 label="Text to use for no-coverage value" 59 label="Text to use for no-coverage value"
60 help="Can be 0.0, N/A, - or any other value. (-filler)" /> 60 help="Can be 0.0, N/A, - or any other value" />
61 <expand macro="print_header" /> 61 <expand macro="print_header" />
62 </inputs> 62 </inputs>
63 <outputs> 63 <outputs>
64 <data name="output" format="bedgraph" /> 64 <data name="output" format="bedgraph" />
65 </outputs> 65 </outputs>
103 <param name="genome_file_opts_selector" value="hist" /> 103 <param name="genome_file_opts_selector" value="hist" />
104 <param name="genome" value="unionBedGraphs1.len" /> 104 <param name="genome" value="unionBedGraphs1.len" />
105 <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" /> 105 <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
106 </test> 106 </test>
107 </tests> 107 </tests>
108 <help> 108 <help><![CDATA[
109 <![CDATA[
110 **What it does** 109 **What it does**
111 110
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. 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.
113 112
114 .. class:: warningmark 113 .. class:: warningmark
227 chr1 450 530 0 0.43 226 chr1 450 530 0 0.43
228 chr1 530 600 Sample2 0.43 227 chr1 530 600 Sample2 0.43
229 chr1 600 700 0 0.43 228 chr1 600 700 0 0.43
230 229
231 @REFERENCES@ 230 @REFERENCES@
232 ]]> 231 ]]></help>
233 </help>
234 <expand macro="citations" /> 232 <expand macro="citations" />
235 </tool> 233 </tool>