annotate bedtools_genomecov/macros.xml @ 3:48e1c3a73761 draft

Uploaded
author jackcurragh
date Fri, 27 May 2022 11:35:46 +0000
parents b63479816ebe
children d0638e3b9667
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
1 <macros>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
2 <xml name="requirements">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
3 <requirements>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
4 <requirement type="package" version="@TOOL_VERSION@">bedtools</requirement>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
5 <yield/>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
6 </requirements>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
7 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
8 <xml name="bio_tools">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
9 <xrefs>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
10 <xref type="bio.tools">bedtools</xref>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
11 </xrefs>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
12 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
13 <token name="@TOOL_VERSION@">2.30.0</token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
14 <token name="@SAMTOOLS_VERSION@">1.9</token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
15 <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf,encodepeak</token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
16 <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
17 <token name="@PROFILE@">20.05</token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
18 <xml name="stdio">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
19 <stdio>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
20 <!-- Anything other than zero is an error -->
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
21 <exit_code range="1:" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
22 <exit_code range=":-1" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
23 <!-- In case the return code has not been set propery check stderr too -->
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
24 <regex match="Error:" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
25 <regex match="Exception:" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
26 </stdio>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
27 <version_command>bedtools --version</version_command>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
28 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
29 <xml name="reciprocal">
b63479816ebe Uploaded
jackcurragh
parents:
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.">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
31 <option value="" selected="true">No</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
32 <option value="-r">Yes</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
33 </param>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
34 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
35 <xml name="fraction" token_name="" token_argument="" token_label="" token_help="" >
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
36 <param name="@NAME@" argument="@ARGUMENT@" type="float" min="0" max="1" optional="true" label="@LABEL@" help="@HELP@" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
37 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
38 <xml name="overlap" token_name="overlap" token_argument="-f" token_fracof="A">
b63479816ebe Uploaded
jackcurragh
parents:
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."/>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
40 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
41 <token name="@OVERLAP@"><![CDATA[
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
42 #if str($overlap):
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
43 -f $overlap
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
44 #end if
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
45 ]]></token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
46 <xml name="strand2">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
47 <param name="strand" type="select" label="Calculation based on strandedness?">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
48 <option value="" selected="true">Overlaps on either strand</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
49 <option value="-s">Only overlaps occurring on the **same** strand.</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
50 <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
51 </param>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
52 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
53 <xml name="seed">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
54 <conditional name="seed">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
55 <param name="seed_choose" type="select" label="Choose Seed?">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
56 <option value="False" selected="true">Random Shuffling</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
57 <option value="True">Choose fixed seed</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
58 </param>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
59 <when value="True">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
60 <param argument="-seed" type="integer" value="12345" label="Enter Seed" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
61 </when>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
62 <when value="False" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
63 </conditional>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
64 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
65 <xml name="split">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
66 <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false"
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
67 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
b63479816ebe Uploaded
jackcurragh
parents:
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." />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
69 </xml>
3
48e1c3a73761 Uploaded
jackcurragh
parents: 0
diff changeset
70 <!-- <xml name="input_conditional_genome_file" token_optional="false" token_help="">
0
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
71 <conditional name="genome_file_opts">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
72 <param name="genome_file_opts_selector" type="select" label="Genome file" help="@HELP@">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
73 <option value="loc" selected="true">Locally installed Genome file</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
74 <option value="hist">Genome file from your history</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
75 </param>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
76 <when value="loc">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
77 <param name="genome" type="select" optional="@OPTIONAL@" multiple="false" label="Genome file">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
78 <options from_data_table="__dbkeys__" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
79 </param>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
80 </when>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
81 <when value="hist">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
82 <param name="genome" type="data" optional="@OPTIONAL@" format="tabular" label="Genome file" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
83 </when>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
84 </conditional>
3
48e1c3a73761 Uploaded
jackcurragh
parents: 0
diff changeset
85 </xml> -->
0
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
86 <token name="@GENOME_FILE@">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
87 #if $genome_file_opts.genome
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
88 -g
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
89 #if $genome_file_opts.genome_file_opts_selector == "loc":
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
90 '$genome_file_opts.genome.fields.len_path'
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
91 #elif $genome_file_opts.genome_file_opts_selector == "hist":
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
92 '$genome_file_opts.genome'
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
93 #end if
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
94 #end if
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
95 </token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
96 <token name="@GENOME_FILE_MAKEWINDOWS@">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
97 #if $type.type_select == "genome":
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
98 #if $type.genome_file_opts.genome_file_opts_selector == "loc":
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
99 -g '$type.genome_file_opts.genome.fields.len_path'
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
100 #elif $type.genome_file_opts.genome_file_opts_selector == "hist":
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
101 -g '$type.genome_file_opts.genome'
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
102 #end if
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
103 #end if
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
104 </token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
105 <token name="@GENOME_FILE_UNION@">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
106 #if $empty.empty_selector == "-empty":
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
107 #if $empty.genome_file_opts.genome_file_opts_selector == "loc":
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
108 -g '$empty.genome_file_opts.genome.fields.len_path'
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
109 #elif $empty.genome_file_opts.genome_file_opts_selector == "hist":
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
110 -g '$empty.genome_file_opts.genome'
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
111 #end if
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
112 #end if
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
113 </token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
114 <token name="@GENOME_FILE_COVERAGE@">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
115 #if $input_type.input_type_select == "bam":
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
116 -ibam '$input_type.input'
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
117 #else:
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
118 -i '$input_type.input'
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
119 #if $input_type.genome_file_opts.genome_file_opts_selector == "loc":
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
120 -g '$input_type.genome_file_opts.genome.fields.len_path'
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
121 #elif $input_type.genome_file_opts.genome_file_opts_selector == "hist":
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
122 -g '$input_type.genome_file_opts.genome'
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
123 #end if
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
124 #end if
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
125 </token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
126 <xml name="closest_D_option">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
127 <param argument="-iu" type="boolean" truevalue="-iu" falsevalue="" checked="false"
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
128 label="Ignore features in B that are upstream of features in A"
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
129 help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
130
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
131 <param argument="-id" type="boolean" truevalue="-id" falsevalue="" checked="false"
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
132 label="Ignore features in B that are downstream of features in A"
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
133 help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
134
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
135 <param argument="-fu" type="boolean" truevalue="-fu" falsevalue="" checked="false"
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
136 label="Choose first from features in B that are upstream of features in A"
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
137 help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
138
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
139 <param argument="-fd" type="boolean" truevalue="-fd" falsevalue="" checked="false"
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
140 label="Choose first from features in B that are downstream of features in A"
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
141 help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
142 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
143 <xml name="addition">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
144 <conditional name="addition">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
145 <param name="addition_select" type="select" label="Choose what you want to do">
b63479816ebe Uploaded
jackcurragh
parents:
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>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
147 <option value="lr">Increase by Start Coordinate and End Coordinate</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
148 </param>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
149 <when value="b">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
150 <param name="b" value="1" label="Number of base pairs" type="integer" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
151 </when>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
152 <when value="lr">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
153 <param name="l" type="integer" value="0" label="The number of base pairs to subtract from the start coordinate" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
154 <param name="r" type="integer" value="0" label="The number of base pairs to add to the end coordinate" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
155 </when>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
156 </conditional>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
157 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
158 <xml name="print_header">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
159 <param argument="-header" type="boolean" truevalue="-header" falsevalue="" checked="false"
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
160 label="Print the header from the A file prior to results" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
161 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
162 <!-- TODO this is currently not used, but we should make use of it -->
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
163 <xml name="genome_validator">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
164 <validator type="unspecified_build" />
b63479816ebe Uploaded
jackcurragh
parents:
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." />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
166 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
167
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
168 <!-- ToDo column_picker -->
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
169 <xml name="choose_columns">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
170 <param name="cols" argument="-c" type="text" value=""
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
171 label="Specify the column(s) that should be summarized"
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
172 help="Comma separated">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
173 <sanitizer invalid_char="">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
174 <valid initial="string.digits"><add value=","/></valid>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
175 </sanitizer>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
176 </param>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
177 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
178
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
179 <token name="@C_AND_O_ARGUMENT@">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
180 #set $col = list()
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
181 #set $op = list()
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
182 #for $item in $c_and_o_argument_repeat:
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
183 #silent $col.append( str($item.col) )
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
184 #silent $op.append( str($item.operation) )
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
185 #end for
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
186 #if $col:
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
187 -c #echo ','.join($col)#
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
188 -o #echo ','.join($op)#
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
189 #end if
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
190 </token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
191
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
192 <xml name="c_and_o_argument">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
193 <repeat name="c_and_o_argument_repeat" title="Applying operations to columns from merged intervals" min="0">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
194 <yield />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
195 <expand macro="choose_operations">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
196 <expand macro="math_options" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
197 <expand macro="additional_math_options" />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
198 </expand>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
199 </repeat>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
200 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
201
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
202 <xml name="choose_operations">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
203 <param name="operation" type="select" label="Specify the operation">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
204 <yield />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
205 </param>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
206 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
207
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
208 <xml name="math_options">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
209 <option value="sum" selected="true">Sum - numeric only</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
210 <option value="min">Min - numeric only</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
211 <option value="max">Max - numeric only</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
212 <option value="absmin">AbsMin - numeric only</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
213 <option value="absmax">AbsMax - numeric only</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
214 <option value="mean">Mean - numeric only</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
215 <option value="median">Median - numeric only</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
216 <option value="mode">Mode - numeric only</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
217 <option value="antimode">Antimode - numeric only</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
218 <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
219 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
220 <xml name="additional_math_options">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
221 <option value="count">Count - numeric or text</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
222 <option value="count_disctinct">Count Distinct - numeric or text</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
223 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
224 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
225 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
226 <xml name="sorted">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
227 <!-- -sorted -g -->
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
228 <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
229 label="For coordinate sorted input file the more efficient sweeping algorithm is enabled."/>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
230 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
231 <token name="@SORTED@">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
232 <![CDATA[
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
233 $sorted
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
234 #if str($sorted) != '':
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
235 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
236 -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
237 #else if str($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'):
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
238 -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
239 #end if
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
240 #end if
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
241 ]]>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
242 </token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
243 <token name="@REFERENCES@">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
244 <![CDATA[
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
245 ------
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
246
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
247 This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_.
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
248
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
249 .. _bedtools package: https://github.com/arq5x/bedtools2
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
250 .. _Quinlan laboratory: http://quinlanlab.org
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
251
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
252
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
253 **Citation**
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
254
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
255 If you use this tool in Galaxy, please cite:
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
256
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
257 Bjoern A. Gruening (2014), `Galaxy wrapper <https://github.com/bgruening/galaxytools>`_
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
258 ]]>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
259 </token>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
260 <xml name="citations">
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
261 <citations>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
262 <citation type="doi">10.1093/bioinformatics/btq033</citation>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
263 <yield />
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
264 </citations>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
265 </xml>
b63479816ebe Uploaded
jackcurragh
parents:
diff changeset
266 </macros>