Mercurial > repos > iuc > bedtools
comparison unionBedGraphs.xml @ 17:44867b59dbf2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
author | iuc |
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date | Tue, 05 Sep 2017 15:40:14 -0400 |
parents | 7308cc546a36 |
children | a8eabd2838f6 |
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16:e0cec48a4695 | 17:44867b59dbf2 |
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1 <tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0"> | 1 <tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.1"> |
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" /> |
8 <command> | 8 <command> |
9 <![CDATA[ | 9 <![CDATA[ |
10 unionBedGraphs | 10 unionBedGraphs |
11 $header | 11 $header |
12 -filler "${filler}" | 12 -filler "${filler}" |
13 #if $zero.value == True: | 13 $empty.empty_selector |
14 -empty | 14 @GENOME_FILE_UNION@ |
15 -g $genome | |
16 #end if | |
17 | 15 |
18 #if str($tag.tag_select) == "tag": | 16 #if str($tag.tag_select) == "tag": |
19 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] ) | 17 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] ) |
20 -i "${files}" | 18 -i "${files}" |
21 #else: | 19 #else: |
41 <param name="inputs" format="bedgraph" type="data" multiple="True" label="BedGraph files" /> | 39 <param name="inputs" format="bedgraph" type="data" multiple="True" label="BedGraph files" /> |
42 </when> | 40 </when> |
43 <when value="custom"> | 41 <when value="custom"> |
44 <repeat name="bedgraphs" title="Add BedGraph files" min="2" > | 42 <repeat name="bedgraphs" title="Add BedGraph files" min="2" > |
45 <param name="input" format="bedgraph" type="data" multiple="True" label="BedGraph file" /> | 43 <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"/> | 44 <param name="custom_name" type="text" area="false" label="Custom sample name" /> |
47 </repeat> | 45 </repeat> |
48 </when> | 46 </when> |
49 </conditional> | 47 </conditional> |
50 <expand macro="genome" /> | 48 <conditional name="empty"> |
51 <param name="zero" type="boolean" checked="true" | 49 <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets"> |
52 label="Report regions with zero coverage" | 50 <option value="-empty">Yes</option> |
53 help="If set, regions without any coverage will also be reported. Requires a valid organism key for all input datasets" /> | 51 <option value="">No</option> |
52 </param> | |
53 <when value="-empty"> | |
54 <expand macro="input_conditional_genome_file" /> | |
55 </when> | |
56 <when value="" /> | |
57 </conditional> | |
54 <param name="filler" type="text" value="N/A" | 58 <param name="filler" type="text" value="N/A" |
55 label="Text to use for no-coverage value" | 59 label="Text to use for no-coverage value" |
56 help="Can be 0.0, N/A, - or any other value. (-filler)" /> | 60 help="Can be 0.0, N/A, - or any other value. (-filler)" /> |
57 <expand macro="print_header" /> | 61 <expand macro="print_header" /> |
58 </inputs> | 62 </inputs> |
59 <outputs> | 63 <outputs> |
60 <data name="output" format="bedgraph" /> | 64 <data name="output" format="bedgraph" /> |
61 </outputs> | 65 </outputs> |
62 <tests> | 66 <tests> |
63 <test> | 67 <test> |
64 <param name="tag_select" value="tag"/> | 68 <param name="tag_select" value="tag" /> |
65 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> | 69 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> |
66 <param name="zero" value="False"/> | 70 <param name="empty_selector" value="" /> |
67 <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" /> | 71 <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" /> |
68 </test> | 72 </test> |
69 <test> | 73 <test> |
70 <param name="tag_select" value="tag"/> | 74 <param name="tag_select" value="tag" /> |
71 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> | 75 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> |
72 <param name="header" value="True"/> | 76 <param name="header" value="True" /> |
73 <param name="zero" value="False"/> | 77 <param name="empty_selector" value="" /> |
74 <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" /> | 78 <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" /> |
75 </test> | 79 </test> |
76 <test> | 80 <test> |
77 <param name="tag_select" value="tag"/> | 81 <param name="tag_select" value="tag" /> |
78 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> | 82 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> |
79 <param name="zero" value="True"/> | 83 <param name="empty_selector" value="-empty" /> |
80 <param name="genome" value="unionBedGraphs1.len"/> | 84 <param name="genome_file_opts_selector" value="hist" /> |
85 <param name="genome" value="unionBedGraphs1.len" /> | |
81 <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" /> | 86 <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" /> |
82 </test> | 87 </test> |
83 <test> | 88 <test> |
84 <param name="tag_select" value="custom"/> | 89 <param name="tag_select" value="custom" /> |
85 <repeat name="bedgraphs"> | 90 <repeat name="bedgraphs"> |
86 <param name="input" value="unionBedGraphs1.bg" /> | 91 <param name="input" value="unionBedGraphs1.bg" /> |
87 <param name="custom_name" value="first" /> | 92 <param name="custom_name" value="first" /> |
88 </repeat> | 93 </repeat> |
89 <repeat name="bedgraphs"> | 94 <repeat name="bedgraphs"> |
92 </repeat> | 97 </repeat> |
93 <repeat name="bedgraphs"> | 98 <repeat name="bedgraphs"> |
94 <param name="input" value="unionBedGraphs3.bg" /> | 99 <param name="input" value="unionBedGraphs3.bg" /> |
95 <param name="custom_name" value="third" /> | 100 <param name="custom_name" value="third" /> |
96 </repeat> | 101 </repeat> |
97 <param name="zero" value="True"/> | 102 <param name="empty_selector" value="-empty" /> |
98 <param name="genome" value="unionBedGraphs1.len"/> | 103 <param name="genome_file_opts_selector" value="hist" /> |
104 <param name="genome" value="unionBedGraphs1.len" /> | |
99 <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" /> | 105 <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" /> |
100 </test> | 106 </test> |
101 </tests> | 107 </tests> |
102 <help> | 108 <help> |
103 <![CDATA[ | 109 <![CDATA[ |