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comparison macros.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
parents b8348686a0b9
children 457b09031d57
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0:b8348686a0b9 1:82aac94b06c3
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.19.1">bedtools</requirement> 4 <requirement type="package" version="2.22">bedtools</requirement>
5 <yield/>
5 </requirements> 6 </requirements>
6 <version_command>bedtools --version</version_command> 7 <version_command>bedtools --version</version_command>
7 </xml> 8 </xml>
8 <token name="@WRAPPER_VERSION@">2.19</token> 9 <token name="@WRAPPER_VERSION@">2.22</token>
9 <xml name="stdio"> 10 <xml name="stdio">
10 <stdio> 11 <stdio>
11 <!-- Anything other than zero is an error --> 12 <!-- Anything other than zero is an error -->
12 <exit_code range="1:" /> 13 <exit_code range="1:" />
13 <exit_code range=":-1" /> 14 <exit_code range=":-1" />
14 <!-- In case the return code has not been set propery check stderr too --> 15 <!-- In case the return code has not been set propery check stderr too -->
15 <regex match="Error:" /> 16 <regex match="Error:" />
16 <regex match="Exception:" /> 17 <regex match="Exception:" />
17 </stdio> 18 </stdio>
18 </xml> 19 </xml>
19 20 <xml name="reciprocal">
21 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
22 label="Require that the fraction of overlap be reciprocal for A and B"
23 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. (-r)" />
24 </xml>
20 <xml name="overlap"> 25 <xml name="overlap">
21 <param name="overlap" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" /> 26 <param name="overlap" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" help="Default is 1E-9, i.e. 1bp. (-f)"/>
22 </xml> 27 </xml>
23 <xml name="strand2"> 28 <xml name="strand2">
24 <param name="strand" type="select" label="Calculation based on strandedness?"> 29 <param name="strand" type="select" label="Calculation based on strandedness?">
25 <option value="" selected="True">Overlaps on either strand</option> 30 <option value="" selected="True">Overlaps on either strand</option>
26 <option value="-s">Only overlaps occurring on the **same** strand.</option> 31 <option value="-s">Only overlaps occurring on the **same** strand.</option>
27 <option value="-S">Only overlaps occurring on the **opposite** strand.</option> 32 <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
28 </param> 33 </param>
29 </xml> 34 </xml>
30 <xml name="seed"> 35 <xml name="seed">
31 <conditional name="seed"> 36 <conditional name="seed">
32 <param name="choose" type="boolean" label="Choose Seed?" selected="False" truevalue="True" falsevalue="False" /> 37 <param name="seed_choose" type="select" label="Choose Seed?" help="(-seed)">
38 <option value="False" selected="True">Random Shuffling</option>
39 <option value="True">Choose fixed seed</option>
40 </param>
33 <when value="True"> 41 <when value="True">
34 <param name="seed" type="integer" value="12345" label="Enter Seed" /> 42 <param name="seed" type="integer" value="12345" label="Enter Seed" />
35 </when> 43 </when>
44 <when value="False" />
36 </conditional> 45 </conditional>
37 </xml> 46 </xml>
38 <xml name="split"> 47 <xml name="split">
39 <param name="split" type="boolean" checked="true" truevalue="-split" falsevalue="" 48 <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue=""
40 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." 49 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
41 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." /> 50 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. (-split)" />
42 </xml> 51 </xml>
43 <xml name="genome"> 52 <xml name="genome">
44 <param format="bed,vcf,gff,gff3" name="genome" type="data" label="Genome file" /> 53 <param format="tabular" name="genome" type="data" label="Genome file" />
54 <!--TODO: make use of: ${chromInfo} -->
45 </xml> 55 </xml>
46 <xml name="addition"> 56 <xml name="addition">
47 <conditional name="addition"> 57 <conditional name="addition">
48 <param name="addition_select" type="select" label="Choose what you want to do"> 58 <param name="addition_select" type="select" label="Choose what you want to do">
49 <option value="b" selected="True">Increase the BED/GFF/VCF entry by the same number base pairs in each direction.</option> 59 <option value="b" selected="True">Increase the BED/GFF/VCF entry by the same number base pairs in each direction.</option>
50 <option value="lr">Increase by Start Coordinate and End Coordinate</option> 60 <option value="lr">Increase by Start Coordinate and End Coordinate</option>
51 </param> 61 </param>
52 <when value="b"> 62 <when value="b">
53 <param name="b" label="Give Value" type="integer" value="0" /> 63 <param name="b" value="1" label="Number of base pairs" type="integer" />
54 </when> 64 </when>
55 <when value="lr"> 65 <when value="lr">
56 <param name="l" label="The number of base pairs to subtract from the start coordinate" type="integer" value="0" /> 66 <param name="l" type="integer" value="0" label="The number of base pairs to subtract from the start coordinate" />
57 <param name="r" label="The number of base pairs to add to the end coordinate" type="integer" value="0" /> 67 <param name="r" type="integer" value="0" label="The number of base pairs to add to the end coordinate" />
58 </when> 68 </when>
59 </conditional> 69 </conditional>
60 </xml> 70 </xml>
71 <xml name="print_header">
72 <param name="header" type="boolean" checked="False" truevalue="-header" falsevalue=""
73 label="Print the header from the A file prior to results" help="(-header)" />
74 </xml>
75 <!-- TODO this is currently not used, but we should make use of it -->
76 <xml name="genome_validator">
77 <validator type="unspecified_build" />
78 <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." />
79 </xml>
80
81 <!-- ToDo column_picker -->
82 <xml name="choose_columns">
83 <param name="cols" type="text" value=""
84 label="Specify the column(s) (comma separated) that should be summarized"
85 help="(-c)">
86 <sanitizer invalid_char="">
87 <valid initial="string.digits"><add value=","/></valid>
88 </sanitizer>
89 </param>
90 </xml>
91
92 <xml name="choose_operations">
93 <param name="operation" type="select" label="Specify the operation">
94 <yield />
95 </param>
96 </xml>
97
61 <xml name="math_options"> 98 <xml name="math_options">
62 <option value="min">Min - numeric only</option> 99 <option value="sum" selected="True">Sum - numeric only</option>
63 <option value="max">Max - numeric only</option> 100 <option value="min">Min - numeric only</option>
64 <option value="mean">Mean - numeric only</option> 101 <option value="max">Max - numeric only</option>
65 <option value="median">Median - numeric only</option> 102 <option value="absmin">AbsMin - numeric only</option>
66 <option value="mode">Mode - numeric only</option> 103 <option value="absmax">AbsMax - numeric only</option>
67 <option value="antimode">Antimode - numeric only</option> 104 <option value="mean">Mean - numeric only</option>
68 <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option> 105 <option value="median">Median - numeric only</option>
69 </xml> 106 <option value="mode">Mode - numeric only</option>
107 <option value="antimode">Antimode - numeric only</option>
108 <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option>
109 </xml>
70 <xml name="additional_math_options"> 110 <xml name="additional_math_options">
71 <option value="count">Count - numeric or text</option> 111 <option value="count">Count - numeric or text</option>
72 <option value="count_disctinct">Count Distinct - numeric or text</option> 112 <option value="count_disctinct">Count Distinct - numeric or text</option>
73 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option> 113 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
74 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option> 114 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
75 </xml> 115 </xml>
76 <token name="@REFERENCES@"> 116 <token name="@REFERENCES@">
117 <![CDATA[
77 ------ 118 ------
78 119
79 This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_. 120 This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_.
80 121
81 .. _bedtools package: https://github.com/arq5x/bedtools2 122 .. _bedtools package: https://github.com/arq5x/bedtools2
82 .. _Quinlan laboratory: http://cphg.virginia.edu/quinlan/ 123 .. _Quinlan laboratory: http://cphg.virginia.edu/quinlan/
83 124
125
126 **Citation**
127
128 If you use this tool in Galaxy, please cite:
129
130 Bjoern A. Gruening (2014), `Galaxy wrapper <https://github.com/bgruening/galaxytools>`_
131 ]]>
84 </token> 132 </token>
85 <xml name="citations"> 133 <xml name="citations">
86 <citations> 134 <citations>
87 <citation type="doi">10.1093/bioinformatics/btq033</citation> 135 <citation type="doi">10.1093/bioinformatics/btq033</citation>
136 <yield />
88 </citations> 137 </citations>
89 </xml> 138 </xml>
90 </macros> 139 </macros>