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comparison macros.xml @ 2:457b09031d57 draft

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author iuc
date Tue, 19 May 2015 07:05:36 -0400
parents 82aac94b06c3
children 2cd7e321d259
comparison
equal deleted inserted replaced
1:82aac94b06c3 2:457b09031d57
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.22">bedtools</requirement> 4 <requirement type="package" version="2.22">bedtools</requirement>
5 <yield/> 5 <yield/>
6 </requirements> 6 </requirements>
7 <version_command>bedtools --version</version_command>
8 </xml> 7 </xml>
9 <token name="@WRAPPER_VERSION@">2.22</token> 8 <token name="@WRAPPER_VERSION@">2.22</token>
10 <xml name="stdio"> 9 <xml name="stdio">
11 <stdio> 10 <stdio>
12 <!-- Anything other than zero is an error --> 11 <!-- Anything other than zero is an error -->
14 <exit_code range=":-1" /> 13 <exit_code range=":-1" />
15 <!-- In case the return code has not been set propery check stderr too --> 14 <!-- In case the return code has not been set propery check stderr too -->
16 <regex match="Error:" /> 15 <regex match="Error:" />
17 <regex match="Exception:" /> 16 <regex match="Exception:" />
18 </stdio> 17 </stdio>
18 <version_command>bedtools --version</version_command>
19 </xml> 19 </xml>
20 <xml name="reciprocal"> 20 <xml name="reciprocal">
21 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" 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" 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)" /> 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)" />
43 </when> 43 </when>
44 <when value="False" /> 44 <when value="False" />
45 </conditional> 45 </conditional>
46 </xml> 46 </xml>
47 <xml name="split"> 47 <xml name="split">
48 <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" 48 <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue=""
49 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."
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)" /> 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)" />
51 </xml> 51 </xml>
52 <xml name="genome"> 52 <xml name="genome">
53 <param format="tabular" name="genome" type="data" label="Genome file" /> 53 <param format="tabular" name="genome" type="data" label="Genome file" />
54 <!--TODO: make use of: ${chromInfo} --> 54 <!--TODO: make use of: ${chromInfo} -->
79 </xml> 79 </xml>
80 80
81 <!-- ToDo column_picker --> 81 <!-- ToDo column_picker -->
82 <xml name="choose_columns"> 82 <xml name="choose_columns">
83 <param name="cols" type="text" value="" 83 <param name="cols" type="text" value=""
84 label="Specify the column(s) (comma separated) that should be summarized" 84 label="Specify the column(s) that should be summarized"
85 help="(-c)"> 85 help="comma separated (-c)">
86 <sanitizer invalid_char=""> 86 <sanitizer invalid_char="">
87 <valid initial="string.digits"><add value=","/></valid> 87 <valid initial="string.digits"><add value=","/></valid>
88 </sanitizer> 88 </sanitizer>
89 </param> 89 </param>
90 </xml> 90 </xml>
91
92 <xml name="choose_column">
93 <param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" />
94 </xml>
95
96 <token name="@C_AND_O_ARGUMENT@">
97 #set $col = list()
98 #set $op = list()
99 #for $item in $c_and_o_argument_repeat:
100 #silent $col.append( str($item.col) )
101 #silent $op.append( str($item.operation) )
102 #end for
103 #if $col:
104 -c #echo ','.join($col)#
105 -o #echo ','.join($op)#
106 #end if
107 </token>
108
109 <xml name="c_and_o_argument">
110 <repeat name="c_and_o_argument_repeat" title="Applying operations to columns from merged intervals" min="0">
111 <expand macro="choose_column" />
112 <expand macro="choose_operations">
113 <expand macro="math_options" />
114 <expand macro="additional_math_options" />
115 </expand>
116 </repeat>
117 </xml>
118
91 119
92 <xml name="choose_operations"> 120 <xml name="choose_operations">
93 <param name="operation" type="select" label="Specify the operation"> 121 <param name="operation" type="select" label="Specify the operation">
94 <yield /> 122 <yield />
95 </param> 123 </param>