annotate bedtools_genomecov/macros.xml @ 0:c00e205995dd draft

Uploaded
author jackcurragh
date Tue, 05 Apr 2022 08:43:05 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
1 <macros>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
2 <xml name="requirements">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
3 <requirements>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
4 <requirement type="package" version="@TOOL_VERSION@">bedtools</requirement>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
5 <yield/>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
6 </requirements>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
7 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
8 <xml name="bio_tools">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
9 <xrefs>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
10 <xref type="bio.tools">bedtools</xref>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
11 </xrefs>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
12 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
13 <token name="@TOOL_VERSION@">2.30.0</token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
14 <token name="@SAMTOOLS_VERSION@">1.9</token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
15 <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf,encodepeak</token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
16 <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
17 <token name="@PROFILE@">20.05</token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
18 <xml name="stdio">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
19 <stdio>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
20 <!-- Anything other than zero is an error -->
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
21 <exit_code range="1:" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
22 <exit_code range=":-1" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
23 <!-- In case the return code has not been set propery check stderr too -->
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
24 <regex match="Error:" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
25 <regex match="Exception:" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
26 </stdio>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
27 <version_command>bedtools --version</version_command>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
28 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
29 <xml name="reciprocal">
c00e205995dd 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.">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
31 <option value="" selected="true">No</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
32 <option value="-r">Yes</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
33 </param>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
34 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
35 <xml name="fraction" token_name="" token_argument="" token_label="" token_help="" >
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
36 <param name="@NAME@" argument="@ARGUMENT@" type="float" min="0" max="1" optional="true" label="@LABEL@" help="@HELP@" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
37 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
38 <xml name="overlap" token_name="overlap" token_argument="-f" token_fracof="A">
c00e205995dd 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."/>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
40 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
41 <token name="@OVERLAP@"><![CDATA[
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
42 #if str($overlap):
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
43 -f $overlap
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
44 #end if
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
45 ]]></token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
46 <xml name="strand2">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
47 <param name="strand" type="select" label="Calculation based on strandedness?">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
48 <option value="" selected="true">Overlaps on either strand</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
49 <option value="-s">Only overlaps occurring on the **same** strand.</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
50 <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
51 </param>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
52 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
53 <xml name="seed">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
54 <conditional name="seed">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
55 <param name="seed_choose" type="select" label="Choose Seed?">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
56 <option value="False" selected="true">Random Shuffling</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
57 <option value="True">Choose fixed seed</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
58 </param>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
59 <when value="True">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
60 <param argument="-seed" type="integer" value="12345" label="Enter Seed" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
61 </when>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
62 <when value="False" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
63 </conditional>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
64 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
65 <xml name="split">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
66 <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false"
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
67 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
c00e205995dd 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." />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
69 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
70 <xml name="input_conditional_genome_file" token_optional="false" token_help="">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
71 <conditional name="genome_file_opts">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
72 <param name="genome_file_opts_selector" type="select" label="Genome file" help="@HELP@">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
73 <option value="loc" selected="true">Locally installed Genome file</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
74 <option value="hist">Genome file from your history</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
75 </param>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
76 <when value="loc">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
77 <param name="genome" type="select" optional="@OPTIONAL@" multiple="false" label="Genome file">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
78 <options from_data_table="__dbkeys__" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
79 </param>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
80 </when>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
81 <when value="hist">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
82 <param name="genome" type="data" optional="@OPTIONAL@" format="tabular" label="Genome file" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
83 </when>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
84 </conditional>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
85 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
86 <token name="@GENOME_FILE@">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
87 #if $genome_file_opts.genome
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
88 -g
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
89 #if $genome_file_opts.genome_file_opts_selector == "loc":
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
90 '$genome_file_opts.genome.fields.len_path'
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
91 #elif $genome_file_opts.genome_file_opts_selector == "hist":
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
92 '$genome_file_opts.genome'
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
93 #end if
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
94 #end if
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
95 </token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
96 <token name="@GENOME_FILE_MAKEWINDOWS@">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
97 #if $type.type_select == "genome":
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
98 #if $type.genome_file_opts.genome_file_opts_selector == "loc":
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
99 -g '$type.genome_file_opts.genome.fields.len_path'
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
100 #elif $type.genome_file_opts.genome_file_opts_selector == "hist":
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
101 -g '$type.genome_file_opts.genome'
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
102 #end if
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
103 #end if
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
104 </token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
105 <token name="@GENOME_FILE_UNION@">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
106 #if $empty.empty_selector == "-empty":
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
107 #if $empty.genome_file_opts.genome_file_opts_selector == "loc":
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
108 -g '$empty.genome_file_opts.genome.fields.len_path'
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
109 #elif $empty.genome_file_opts.genome_file_opts_selector == "hist":
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
110 -g '$empty.genome_file_opts.genome'
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
111 #end if
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
112 #end if
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
113 </token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
114 <token name="@GENOME_FILE_COVERAGE@">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
115 #if $input_type.input_type_select == "bam":
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
116 -ibam '$input_type.input'
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
117 #else:
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
118 -i '$input_type.input'
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
119 #if $input_type.genome_file_opts.genome_file_opts_selector == "loc":
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
120 -g '$input_type.genome_file_opts.genome.fields.len_path'
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
121 #elif $input_type.genome_file_opts.genome_file_opts_selector == "hist":
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
122 -g '$input_type.genome_file_opts.genome'
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
123 #end if
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
124 #end if
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
125 </token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
126 <xml name="closest_D_option">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
127 <param argument="-iu" type="boolean" truevalue="-iu" falsevalue="" checked="false"
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
128 label="Ignore features in B that are upstream of features in A"
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
129 help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
130
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
131 <param argument="-id" type="boolean" truevalue="-id" falsevalue="" checked="false"
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
132 label="Ignore features in B that are downstream of features in A"
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
133 help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
134
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
135 <param argument="-fu" type="boolean" truevalue="-fu" falsevalue="" checked="false"
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
136 label="Choose first from features in B that are upstream of features in A"
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
137 help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
138
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
139 <param argument="-fd" type="boolean" truevalue="-fd" falsevalue="" checked="false"
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
140 label="Choose first from features in B that are downstream of features in A"
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
141 help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
142 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
143 <xml name="addition">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
144 <conditional name="addition">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
145 <param name="addition_select" type="select" label="Choose what you want to do">
c00e205995dd 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>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
147 <option value="lr">Increase by Start Coordinate and End Coordinate</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
148 </param>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
149 <when value="b">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
150 <param name="b" value="1" label="Number of base pairs" type="integer" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
151 </when>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
152 <when value="lr">
c00e205995dd 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" />
c00e205995dd 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" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
155 </when>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
156 </conditional>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
157 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
158 <xml name="print_header">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
159 <param argument="-header" type="boolean" truevalue="-header" falsevalue="" checked="false"
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
160 label="Print the header from the A file prior to results" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
161 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
162 <!-- TODO this is currently not used, but we should make use of it -->
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
163 <xml name="genome_validator">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
164 <validator type="unspecified_build" />
c00e205995dd 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." />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
166 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
167
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
168 <!-- ToDo column_picker -->
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
169 <xml name="choose_columns">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
170 <param name="cols" argument="-c" type="text" value=""
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
171 label="Specify the column(s) that should be summarized"
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
172 help="Comma separated">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
173 <sanitizer invalid_char="">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
174 <valid initial="string.digits"><add value=","/></valid>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
175 </sanitizer>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
176 </param>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
177 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
178
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
179 <token name="@C_AND_O_ARGUMENT@">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
180 #set $col = list()
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
181 #set $op = list()
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
182 #for $item in $c_and_o_argument_repeat:
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
183 #silent $col.append( str($item.col) )
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
184 #silent $op.append( str($item.operation) )
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
185 #end for
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
186 #if $col:
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
187 -c #echo ','.join($col)#
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
188 -o #echo ','.join($op)#
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
189 #end if
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
190 </token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
191
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
192 <xml name="c_and_o_argument">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
193 <repeat name="c_and_o_argument_repeat" title="Applying operations to columns from merged intervals" min="0">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
194 <yield />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
195 <expand macro="choose_operations">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
196 <expand macro="math_options" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
197 <expand macro="additional_math_options" />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
198 </expand>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
199 </repeat>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
200 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
201
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
202 <xml name="choose_operations">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
203 <param name="operation" type="select" label="Specify the operation">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
204 <yield />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
205 </param>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
206 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
207
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
208 <xml name="math_options">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
209 <option value="sum" selected="true">Sum - numeric only</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
210 <option value="min">Min - numeric only</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
211 <option value="max">Max - numeric only</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
212 <option value="absmin">AbsMin - numeric only</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
213 <option value="absmax">AbsMax - numeric only</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
214 <option value="mean">Mean - numeric only</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
215 <option value="median">Median - numeric only</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
216 <option value="mode">Mode - numeric only</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
217 <option value="antimode">Antimode - numeric only</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
218 <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
219 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
220 <xml name="additional_math_options">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
221 <option value="count">Count - numeric or text</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
222 <option value="count_disctinct">Count Distinct - numeric or text</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
223 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
224 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
225 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
226 <xml name="sorted">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
227 <!-- -sorted -g -->
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
228 <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
229 label="For coordinate sorted input file the more efficient sweeping algorithm is enabled."/>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
230 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
231 <token name="@SORTED@">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
232 <![CDATA[
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
233 $sorted
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
234 #if str($sorted) != '':
c00e205995dd 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'):
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
236 -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
237 #else if str($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'):
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
238 -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
239 #end if
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
240 #end if
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
241 ]]>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
242 </token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
243 <token name="@REFERENCES@">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
244 <![CDATA[
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
245 ------
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
246
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
247 This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_.
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
248
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
249 .. _bedtools package: https://github.com/arq5x/bedtools2
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
250 .. _Quinlan laboratory: http://quinlanlab.org
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
251
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
252
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
253 **Citation**
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
254
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
255 If you use this tool in Galaxy, please cite:
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
256
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
257 Bjoern A. Gruening (2014), `Galaxy wrapper <https://github.com/bgruening/galaxytools>`_
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
258 ]]>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
259 </token>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
260 <xml name="citations">
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
261 <citations>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
262 <citation type="doi">10.1093/bioinformatics/btq033</citation>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
263 <yield />
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
264 </citations>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
265 </xml>
c00e205995dd Uploaded
jackcurragh
parents:
diff changeset
266 </macros>