annotate macros.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 07e8b80f278c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
1 <macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
2 <xml name="requirements">
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
3 <requirements>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
4 <requirement type="package" version="@TOOL_VERSION@">bedtools</requirement>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
5 <yield/>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
6 </requirements>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
7 </xml>
39
3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 37
diff changeset
8 <xml name="bio_tools">
3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 37
diff changeset
9 <xrefs>
3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 37
diff changeset
10 <xref type="bio.tools">bedtools</xref>
3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 37
diff changeset
11 </xrefs>
3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 37
diff changeset
12 </xml>
46
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 43
diff changeset
13 <token name="@TOOL_VERSION@">2.31.1</token>
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 27
diff changeset
14 <token name="@SAMTOOLS_VERSION@">1.9</token>
36
0a5c785ac6db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 833a0b5510d91226c1b0b94550cebfd44243b8d4"
iuc
parents: 35
diff changeset
15 <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf,encodepeak</token>
0a5c785ac6db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 833a0b5510d91226c1b0b94550cebfd44243b8d4"
iuc
parents: 35
diff changeset
16 <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token>
39
3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 37
diff changeset
17 <token name="@PROFILE@">20.05</token>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
18 <xml name="stdio">
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
19 <stdio>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
20 <!-- Anything other than zero is an error -->
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
21 <exit_code range="1:" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
22 <exit_code range=":-1" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
23 <!-- In case the return code has not been set propery check stderr too -->
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
24 <regex match="Error:" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
25 <regex match="Exception:" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
26 </stdio>
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
27 <version_command>bedtools --version</version_command>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
28 </xml>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
29 <xml name="reciprocal">
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 27
diff changeset
30 <param name="reciprocal" argument="-r" type="select" label="Require that the fraction of overlap be reciprocal for A and B" help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
31 <option value="" selected="true">No</option>
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 27
diff changeset
32 <option value="-r">Yes</option>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 27
diff changeset
33 </param>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
34 </xml>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
35 <xml name="fraction" token_name="" token_argument="" token_label="" token_help="" >
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
36 <param name="@NAME@" argument="@ARGUMENT@" type="float" min="0" max="1" optional="true" label="@LABEL@" help="@HELP@" />
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
37 </xml>
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
38 <xml name="overlap" token_name="overlap" token_argument="-f" token_fracof="A">
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
39 <expand macro="fraction" name="@NAME@" argument="@ARGUMENT@" label="Minimum overlap required as a fraction of @FRACOF@" help="Default is 1E-9, i.e. 1bp."/>
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 27
diff changeset
40 </xml>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
41 <token name="@OVERLAP@"><![CDATA[
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
42 #if str($overlap):
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
43 -f $overlap
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
44 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
45 ]]></token>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
46 <xml name="strand2">
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
47 <param name="strand" type="select" label="Calculation based on strandedness?">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
48 <option value="" selected="true">Overlaps on either strand</option>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
49 <option value="-s">Only overlaps occurring on the **same** strand.</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
50 <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
51 </param>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
52 </xml>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
53 <xml name="seed">
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
54 <conditional name="seed">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
55 <param name="seed_choose" type="select" label="Choose Seed?">
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
56 <option value="False" selected="true">Random Shuffling</option>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
57 <option value="True">Choose fixed seed</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
58 </param>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
59 <when value="True">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
60 <param argument="-seed" type="integer" value="12345" label="Enter Seed" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
61 </when>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
62 <when value="False" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
63 </conditional>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
64 </xml>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
65 <xml name="split">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
66 <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false"
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
67 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
68 help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
69 </xml>
43
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 39
diff changeset
70 <xml name="input_conditional_genome_file" token_optional="false" token_help="">
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
71 <conditional name="genome_file_opts">
43
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 39
diff changeset
72 <param name="genome_file_opts_selector" type="select" label="Genome file" help="@HELP@">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
73 <option value="loc" selected="true">Locally installed Genome file</option>
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
74 <option value="hist">Genome file from your history</option>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
75 </param>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
76 <when value="loc">
43
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 39
diff changeset
77 <param name="genome" type="select" optional="@OPTIONAL@" multiple="false" label="Genome file">
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
78 <options from_data_table="__dbkeys__" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
79 </param>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
80 </when>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
81 <when value="hist">
43
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 39
diff changeset
82 <param name="genome" type="data" optional="@OPTIONAL@" format="tabular" label="Genome file" />
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
83 </when>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
84 </conditional>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
85 </xml>
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
86 <token name="@GENOME_FILE@">
43
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 39
diff changeset
87 #if $genome_file_opts.genome
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 39
diff changeset
88 -g
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 39
diff changeset
89 #if $genome_file_opts.genome_file_opts_selector == "loc":
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 39
diff changeset
90 '$genome_file_opts.genome.fields.len_path'
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 39
diff changeset
91 #elif $genome_file_opts.genome_file_opts_selector == "hist":
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 39
diff changeset
92 '$genome_file_opts.genome'
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
93 #end if
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
94 #end if
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
95 </token>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
96 <token name="@GENOME_FILE_MAKEWINDOWS@">
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
97 #if $type.type_select == "genome":
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
98 #if $type.genome_file_opts.genome_file_opts_selector == "loc":
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
99 -g '$type.genome_file_opts.genome.fields.len_path'
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
100 #elif $type.genome_file_opts.genome_file_opts_selector == "hist":
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
101 -g '$type.genome_file_opts.genome'
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
102 #end if
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
103 #end if
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
104 </token>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
105 <token name="@GENOME_FILE_UNION@">
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
106 #if $empty.empty_selector == "-empty":
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
107 #if $empty.genome_file_opts.genome_file_opts_selector == "loc":
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
108 -g '$empty.genome_file_opts.genome.fields.len_path'
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
109 #elif $empty.genome_file_opts.genome_file_opts_selector == "hist":
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
110 -g '$empty.genome_file_opts.genome'
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
111 #end if
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
112 #end if
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
113 </token>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
114 <token name="@GENOME_FILE_COVERAGE@">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
115 #if $input_type.input_type_select == "bam":
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
116 -ibam '$input_type.input'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
117 #else:
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
118 -i '$input_type.input'
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
119 #if $input_type.genome_file_opts.genome_file_opts_selector == "loc":
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
120 -g '$input_type.genome_file_opts.genome.fields.len_path'
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
121 #elif $input_type.genome_file_opts.genome_file_opts_selector == "hist":
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
122 -g '$input_type.genome_file_opts.genome'
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
123 #end if
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
124 #end if
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 14
diff changeset
125 </token>
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 3
diff changeset
126 <xml name="closest_D_option">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
127 <param argument="-iu" type="boolean" truevalue="-iu" falsevalue="" checked="false"
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
128 label="Ignore features in B that are upstream of features in A"
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
129 help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 3
diff changeset
130
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
131 <param argument="-id" type="boolean" truevalue="-id" falsevalue="" checked="false"
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
132 label="Ignore features in B that are downstream of features in A"
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
133 help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 3
diff changeset
134
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
135 <param argument="-fu" type="boolean" truevalue="-fu" falsevalue="" checked="false"
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
136 label="Choose first from features in B that are upstream of features in A"
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
137 help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 3
diff changeset
138
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
139 <param argument="-fd" type="boolean" truevalue="-fd" falsevalue="" checked="false"
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
140 label="Choose first from features in B that are downstream of features in A"
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
141 help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 3
diff changeset
142 </xml>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
143 <xml name="addition">
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
144 <conditional name="addition">
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
145 <param name="addition_select" type="select" label="Choose what you want to do">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
146 <option value="b" selected="true">Increase the @STD_BEDTOOLS_INPUT_LABEL@ entry by the same number base pairs in each direction.</option>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
147 <option value="lr">Increase by Start Coordinate and End Coordinate</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
148 </param>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
149 <when value="b">
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
150 <param name="b" value="1" label="Number of base pairs" type="integer" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
151 </when>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
152 <when value="lr">
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
153 <param name="l" type="integer" value="0" label="The number of base pairs to subtract from the start coordinate" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
154 <param name="r" type="integer" value="0" label="The number of base pairs to add to the end coordinate" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
155 </when>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
156 </conditional>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
157 </xml>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
158 <xml name="print_header">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
159 <param argument="-header" type="boolean" truevalue="-header" falsevalue="" checked="false"
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
160 label="Print the header from the A file prior to results" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
161 </xml>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
162 <!-- TODO this is currently not used, but we should make use of it -->
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
163 <xml name="genome_validator">
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
164 <validator type="unspecified_build" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
165 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
166 </xml>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
167
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
168 <!-- ToDo column_picker -->
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
169 <xml name="choose_columns">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
170 <param name="cols" argument="-c" type="text" value=""
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
171 label="Specify the column(s) that should be summarized"
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
172 help="Comma separated">
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
173 <sanitizer invalid_char="">
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
174 <valid initial="string.digits"><add value=","/></valid>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
175 </sanitizer>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
176 </param>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
177 </xml>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
178
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
179 <token name="@C_AND_O_ARGUMENT@">
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
180 #set $col = list()
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
181 #set $op = list()
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
182 #for $item in $c_and_o_argument_repeat:
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
183 #silent $col.append( str($item.col) )
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
184 #silent $op.append( str($item.operation) )
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
185 #end for
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
186 #if $col:
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
187 -c #echo ','.join($col)#
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
188 -o #echo ','.join($op)#
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
189 #end if
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
190 </token>
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
191
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
192 <xml name="c_and_o_argument">
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
193 <repeat name="c_and_o_argument_repeat" title="Applying operations to columns from merged intervals" min="0">
3
2cd7e321d259 Uploaded
iuc
parents: 2
diff changeset
194 <yield />
2
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
195 <expand macro="choose_operations">
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
196 <expand macro="math_options" />
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
197 <expand macro="additional_math_options" />
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
198 </expand>
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
199 </repeat>
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
200 </xml>
457b09031d57 Uploaded
iuc
parents: 1
diff changeset
201
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
202 <xml name="choose_operations">
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
203 <param name="operation" type="select" label="Specify the operation">
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
204 <yield />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
205 </param>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
206 </xml>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
207
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
208 <xml name="math_options">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
209 <option value="sum" selected="true">Sum - numeric only</option>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
210 <option value="min">Min - numeric only</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
211 <option value="max">Max - numeric only</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
212 <option value="absmin">AbsMin - numeric only</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
213 <option value="absmax">AbsMax - numeric only</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
214 <option value="mean">Mean - numeric only</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
215 <option value="median">Median - numeric only</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
216 <option value="mode">Mode - numeric only</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
217 <option value="antimode">Antimode - numeric only</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
218 <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
219 </xml>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
220 <xml name="additional_math_options">
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
221 <option value="count">Count - numeric or text</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
222 <option value="count_disctinct">Count Distinct - numeric or text</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
223 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
224 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
225 </xml>
37
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
226 <xml name="sorted">
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
227 <!-- -sorted -g -->
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
228 <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
229 label="For coordinate sorted input file the more efficient sweeping algorithm is enabled."/>
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
230 </xml>
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
231 <token name="@SORTED@">
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
232 <![CDATA[
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
233 $sorted
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
234 #if str($sorted) != '':
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
235 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
236 -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
237 #else if str($reduce_or_iterate.reduce_or_iterate_selector) == 'reduce' and str($reduce_or_iterate.inputB) != 'None' and $reduce_or_iterate.inputB[0].is_of_type('bam'):
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
238 -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
239 #end if
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
240 #end if
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
241 ]]>
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 36
diff changeset
242 </token>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
243 <token name="@REFERENCES@">
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
244 <![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
245 ------
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
246
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
247 This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
248
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
249 .. _bedtools package: https://github.com/arq5x/bedtools2
13
fadebae7e69b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 391d2d41095edb2badf70924d3636238453ee377
iuc
parents: 11
diff changeset
250 .. _Quinlan laboratory: http://quinlanlab.org
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
251
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
252
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
253 **Citation**
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
254
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
255 If you use this tool in Galaxy, please cite:
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
256
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
257 Bjoern A. Gruening (2014), `Galaxy wrapper <https://github.com/bgruening/galaxytools>`_
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
258 ]]>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
259 </token>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
260 <xml name="citations">
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
261 <citations>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
262 <citation type="doi">10.1093/bioinformatics/btq033</citation>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
263 <yield />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
264 </citations>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
265 </xml>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
266 </macros>