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comparison unionBedGraphs.xml @ 4:315929597efb draft

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author iuc
date Wed, 07 Jan 2015 12:45:05 -0500
parents 7511823bdea1
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3:190a747ddaa8 4:315929597efb
1 <tool id="bedtools_mergebedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0">
2 <description></description> 2 <description></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>unionBedGraphs 8 <command>
9 <![CDATA[
10 unionBedGraphs
9 $header 11 $header
10 -filler '$filler' 12 -filler "${filler}"
11 #if $zero.value == True: 13 #if $zero.value == True:
12 -empty 14 -empty
13 -g ${chromInfo} 15 -g $genome
14 #end if 16 #end if
15 17
16 -i '$input1' 18 #if str($tag.tag_select) == "tag":
17 '$input2' 19 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
18 #for $q in $bedgraphs 20 -i "${files}"
19 '${q.input}' 21 #else:
20 #end for 22 -i
21 23 #for $bg in $tag.bedgraphs:
22 -names 24 "${bg.input}"
23 #if $name1.choice == "tag": 25 #end for
24 '${input1.name}' 26 -names
25 #else 27 #for $bg in $tag.bedgraphs:
26 '${name1.custom_name}' 28 "${bg.custom_name}"
29 #end for
27 #end if 30 #end if
28 31 > "${output}"
29 #if $name2.choice == "tag": 32 ]]>
30 '${input2.name}'
31 #else
32 '${name2.custom_name}'
33 #end if
34
35 #for $q in $bedgraphs
36 #if $q.name.choice == "tag":
37 '${q.input.name}'
38 #else
39 '${q.input.custom_name}'
40 #end if
41 #end for
42 &gt; '$output'
43 </command> 33 </command>
44 <inputs> 34 <inputs>
45 <!-- Make it easy for the user, first two input files are always shown --> 35 <conditional name="tag">
46 <!-- INPUT 1 --> 36 <param name="tag_select" type="select" label="Sample name">
47 <param name="input1" format="bedgraph" type="data" label="First BedGraph file" />
48
49 <conditional name="name1">
50 <param name="choice" type="select" label="Sample name">
51 <option value="tag" selected="true">Use input's tag</option> 37 <option value="tag" selected="true">Use input's tag</option>
52 <option value="custom">Enter custom table name</option> 38 <option value="custom">Enter custom name per file</option>
53 </param> 39 </param>
54 <when value="tag"> 40 <when value="tag">
41 <param name="inputs" format="bedgraph" type="data" multiple="True" label="BedGraph files" />
55 </when> 42 </when>
56 <when value="custom"> 43 <when value="custom">
57 <param name="custom_name" type="text" area="false" label="Custom sample name"/> 44 <repeat name="bedgraphs" title="Add BedGraph files" min="2" >
45 <param name="input" format="bedgraph" type="data" multiple="True" label="BedGraph file" />
46 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
47 </repeat>
58 </when> 48 </when>
59 </conditional> 49 </conditional>
60 50 <expand macro="genome" />
61 <!-- INPUT 2 --> 51 <param name="zero" type="boolean" checked="true"
62 <param name="input2" format="bedgraph" type="data" label="Second BedGraph file" /> 52 label="Report regions with zero coverage"
63 53 help="If set, regions without any coverage will also be reported. Requires a valid organism key for all input datasets" />
64 <conditional name="name2"> 54 <param name="filler" type="text" value="N/A"
65 <param name="choice" type="select" label="Sample name"> 55 label="Text to use for no-coverage value"
66 <option value="tag" selected="true">Use input's tag</option> 56 help="Can be 0.0, N/A, - or any other value. (-filler)" />
67 <option value="custom">Enter custom table name</option> 57 <expand macro="print_header" />
68 </param>
69 <when value="tag">
70 </when>
71 <when value="custom">
72 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
73 </when>
74 </conditional>
75
76 <!-- Additional files, if the user needs more -->
77 <repeat name="bedgraphs" title="Add'l BedGraph files" >
78 <param name="input" format="bedgraph" type="data" label="BedGraph file" />
79 <conditional name="name">
80 <param name="choice" type="select" label="Sample name">
81 <option value="tag" selected="true">Use input's tag</option>
82 <option value="custom">Enter custom table name</option>
83 </param>
84 <when value="tag">
85 </when>
86 <when value="custom">
87 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
88 </when>
89 </conditional>
90 </repeat>
91
92 <param name="header" type="boolean" checked="true" truevalue="-header" falsevalue="" label="Print header line" help="The first line will include the name of each sample." />
93
94 <param name="zero" type="boolean" checked="true" label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported. Requires a valid organism key for all input datasets" />
95
96 <param name="filler" type="text" value="0" label="Text to use for no-coverage value" help="Can be 0.0, N/A, - or any other value." />
97 </inputs> 58 </inputs>
98
99 <outputs> 59 <outputs>
100 <data format="tabular" name="output" metadata_source="input1" label="Merged BedGraphs of ${input1.name}, ${input2.name} and so on." /> 60 <data name="output" format="bedgraph" />
101 </outputs> 61 </outputs>
62 <tests>
63 <test>
64 <param name="tag_select" value="tag"/>
65 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
66 <param name="zero" value="False"/>
67 <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" />
68 </test>
69 <test>
70 <param name="tag_select" value="tag"/>
71 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
72 <param name="header" value="True"/>
73 <param name="zero" value="False"/>
74 <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" />
75 </test>
76 <test>
77 <param name="tag_select" value="tag"/>
78 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
79 <param name="zero" value="True"/>
80 <param name="genome" value="unionBedGraphs1.len"/>
81 <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" />
82 </test>
83 <test>
84 <param name="tag_select" value="custom"/>
85 <repeat name="bedgraphs">
86 <param name="input" value="unionBedGraphs1.bg" />
87 <param name="custom_name" value="first" />
88 </repeat>
89 <repeat name="bedgraphs">
90 <param name="input" value="unionBedGraphs2.bg" />
91 <param name="custom_name" value="second" />
92 </repeat>
93 <repeat name="bedgraphs">
94 <param name="input" value="unionBedGraphs3.bg" />
95 <param name="custom_name" value="third" />
96 </repeat>
97 <param name="zero" value="True"/>
98 <param name="genome" value="unionBedGraphs1.len"/>
99 <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
100 </test>
101 </tests>
102 <help> 102 <help>
103 103 <![CDATA[
104 **What it does** 104 **What it does**
105 105
106 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. 106 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.
107 107
108 .. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/ubg.png 108 .. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/ubg.png
224 chr1 450 530 0 0.43 224 chr1 450 530 0 0.43
225 chr1 530 600 Sample2 0.43 225 chr1 530 600 Sample2 0.43
226 chr1 600 700 0 0.43 226 chr1 600 700 0 0.43
227 227
228 @REFERENCES@ 228 @REFERENCES@
229 229 ]]>
230 </help> 230 </help>
231 <expand macro="citations" /> 231 <expand macro="citations" />
232 </tool> 232 </tool>