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comparison macros.xml @ 34:dde39ba9c031 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:55:48 -0400
parents 4f7a5ccd2ae9
children b28e0cfa7ba1
comparison
equal deleted inserted replaced
33:87ee588b3d45 34:dde39ba9c031
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="@WRAPPER_VERSION@">bedtools</requirement> 4 <requirement type="package" version="@TOOL_VERSION@">bedtools</requirement>
5 <yield/> 5 <yield/>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8 <token name="@WRAPPER_VERSION@">2.27.1</token> 8 <token name="@TOOL_VERSION@">2.27.1</token>
9 <token name="@SAMTOOLS_VERSION@">1.9</token> 9 <token name="@SAMTOOLS_VERSION@">1.9</token>
10 <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf</token> 10 <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf</token>
11 <token name="@STD_BEDTOOLS_INPUT_LABEL@">bed,bedgraph,gff,vcf</token> 11 <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF</token>
12 <xml name="stdio"> 12 <xml name="stdio">
13 <stdio> 13 <stdio>
14 <!-- Anything other than zero is an error --> 14 <!-- Anything other than zero is an error -->
15 <exit_code range="1:" /> 15 <exit_code range="1:" />
16 <exit_code range=":-1" /> 16 <exit_code range=":-1" />
20 </stdio> 20 </stdio>
21 <version_command>bedtools --version</version_command> 21 <version_command>bedtools --version</version_command>
22 </xml> 22 </xml>
23 <xml name="reciprocal"> 23 <xml name="reciprocal">
24 <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."> 24 <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.">
25 <option value="" selected="True">No</option> 25 <option value="" selected="true">No</option>
26 <option value="-r">Yes</option> 26 <option value="-r">Yes</option>
27 </param> 27 </param>
28 </xml> 28 </xml>
29 <xml name="overlap"> 29 <xml name="fraction" token_name="" token_argument="" token_label="" token_help="" >
30 <param name="overlap" argument="-f" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" help="Default is 1E-9, i.e. 1bp."/> 30 <param name="@NAME@" argument="@ARGUMENT@" type="float" min="0" max="1" optional="true" label="@LABEL@" help="@HELP@" />
31 </xml> 31 </xml>
32 <xml name="overlapB"> 32 <xml name="overlap" token_name="overlap" token_argument="-f" token_fracof="A">
33 <param name="overlapB" argument="-F" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" help="Default is 1E-9, i.e. 1bp."/> 33 <expand macro="fraction" name="@NAME@" argument="@ARGUMENT@" label="Minimum overlap required as a fraction of @FRACOF@" help="Default is 1E-9, i.e. 1bp."/>
34 </xml> 34 </xml>
35 <token name="@OVERLAP@"><![CDATA[
36 #if str($overlap):
37 -f $overlap
38 #end if
39 ]]></token>
35 <xml name="strand2"> 40 <xml name="strand2">
36 <param name="strand" type="select" label="Calculation based on strandedness?"> 41 <param name="strand" type="select" label="Calculation based on strandedness?">
37 <option value="" selected="True">Overlaps on either strand</option> 42 <option value="" selected="true">Overlaps on either strand</option>
38 <option value="-s">Only overlaps occurring on the **same** strand.</option> 43 <option value="-s">Only overlaps occurring on the **same** strand.</option>
39 <option value="-S">Only overlaps occurring on the **opposite** strand.</option> 44 <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
40 </param> 45 </param>
41 </xml> 46 </xml>
42 <xml name="seed"> 47 <xml name="seed">
43 <conditional name="seed"> 48 <conditional name="seed">
44 <param name="seed_choose" type="select" label="Choose Seed?" help="(-seed)"> 49 <param name="seed_choose" type="select" label="Choose Seed?">
45 <option value="False" selected="True">Random Shuffling</option> 50 <option value="False" selected="true">Random Shuffling</option>
46 <option value="True">Choose fixed seed</option> 51 <option value="True">Choose fixed seed</option>
47 </param> 52 </param>
48 <when value="True"> 53 <when value="True">
49 <param name="seed" type="integer" value="12345" label="Enter Seed" /> 54 <param argument="-seed" type="integer" value="12345" label="Enter Seed" />
50 </when> 55 </when>
51 <when value="False" /> 56 <when value="False" />
52 </conditional> 57 </conditional>
53 </xml> 58 </xml>
54 <xml name="split"> 59 <xml name="split">
55 <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" 60 <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false"
56 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." 61 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
57 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)" /> 62 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." />
58 </xml> 63 </xml>
59 <xml name="input_conditional_genome_file"> 64 <xml name="input_conditional_genome_file">
60 <conditional name="genome_file_opts"> 65 <conditional name="genome_file_opts">
61 <param name="genome_file_opts_selector" type="select" label="Genome file"> 66 <param name="genome_file_opts_selector" type="select" label="Genome file">
62 <option value="loc" selected="True">Locally installed Genome file</option> 67 <option value="loc" selected="true">Locally installed Genome file</option>
63 <option value="hist">Genome file from your history</option> 68 <option value="hist">Genome file from your history</option>
64 </param> 69 </param>
65 <when value="loc"> 70 <when value="loc">
66 <param name="genome" type="select" multiple="false" label="Genome file"> 71 <param name="genome" type="select" multiple="false" label="Genome file">
67 <options from_data_table="__dbkeys__" /> 72 <options from_data_table="__dbkeys__" />
105 -g '$empty.genome_file_opts.genome' 110 -g '$empty.genome_file_opts.genome'
106 #end if 111 #end if
107 #end if 112 #end if
108 </token> 113 </token>
109 <token name="@GENOME_FILE_COVERAGE@"> 114 <token name="@GENOME_FILE_COVERAGE@">
110 #if $input_type.input_type_select == "bed": 115 #if $input_type.input_type_select == "bam":
116 -ibam '$input_type.input'
117 #else:
111 -i '$input_type.input' 118 -i '$input_type.input'
112 #if $input_type.genome_file_opts.genome_file_opts_selector == "loc": 119 #if $input_type.genome_file_opts.genome_file_opts_selector == "loc":
113 -g '$input_type.genome_file_opts.genome.fields.len_path' 120 -g '$input_type.genome_file_opts.genome.fields.len_path'
114 #elif $input_type.genome_file_opts.genome_file_opts_selector == "hist": 121 #elif $input_type.genome_file_opts.genome_file_opts_selector == "hist":
115 -g '$input_type.genome_file_opts.genome' 122 -g '$input_type.genome_file_opts.genome'
116 #end if 123 #end if
117 #elif $input_type.input_type_select == "bam":
118 -ibam '$input_type.input'
119 #end if 124 #end if
120 </token> 125 </token>
121 <xml name="closest_D_option"> 126 <xml name="closest_D_option">
122 <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" 127 <param argument="-iu" type="boolean" truevalue="-iu" falsevalue="" checked="false"
123 label="Ignore features in B that are upstream of features in A" 128 label="Ignore features in B that are upstream of features in A"
124 help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" /> 129 help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
125 130
126 <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue="" 131 <param argument="-id" type="boolean" truevalue="-id" falsevalue="" checked="false"
127 label="Ignore features in B that are downstream of features in A" 132 label="Ignore features in B that are downstream of features in A"
128 help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" /> 133 help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
129 134
130 <param name="fu" type="boolean" checked="false" truevalue="-fu" falsevalue="" 135 <param argument="-fu" type="boolean" truevalue="-fu" falsevalue="" checked="false"
131 label="Choose first from features in B that are upstream of features in A" 136 label="Choose first from features in B that are upstream of features in A"
132 help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-fu)" /> 137 help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
133 138
134 <param name="fd" type="boolean" checked="false" truevalue="-fd" falsevalue="" 139 <param argument="-fd" type="boolean" truevalue="-fd" falsevalue="" checked="false"
135 label="Choose first from features in B that are downstream of features in A" 140 label="Choose first from features in B that are downstream of features in A"
136 help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-fd)" /> 141 help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
137 </xml> 142 </xml>
138 <xml name="addition"> 143 <xml name="addition">
139 <conditional name="addition"> 144 <conditional name="addition">
140 <param name="addition_select" type="select" label="Choose what you want to do"> 145 <param name="addition_select" type="select" label="Choose what you want to do">
141 <option value="b" selected="True">Increase the @STD_BEDTOOLS_INPUT_LABEL@ entry by the same number base pairs in each direction.</option> 146 <option value="b" selected="true">Increase the @STD_BEDTOOLS_INPUT_LABEL@ entry by the same number base pairs in each direction.</option>
142 <option value="lr">Increase by Start Coordinate and End Coordinate</option> 147 <option value="lr">Increase by Start Coordinate and End Coordinate</option>
143 </param> 148 </param>
144 <when value="b"> 149 <when value="b">
145 <param name="b" value="1" label="Number of base pairs" type="integer" /> 150 <param name="b" value="1" label="Number of base pairs" type="integer" />
146 </when> 151 </when>
149 <param name="r" type="integer" value="0" label="The number of base pairs to add to the end coordinate" /> 154 <param name="r" type="integer" value="0" label="The number of base pairs to add to the end coordinate" />
150 </when> 155 </when>
151 </conditional> 156 </conditional>
152 </xml> 157 </xml>
153 <xml name="print_header"> 158 <xml name="print_header">
154 <param name="header" type="boolean" checked="False" truevalue="-header" falsevalue="" 159 <param argument="-header" type="boolean" truevalue="-header" falsevalue="" checked="false"
155 label="Print the header from the A file prior to results" help="(-header)" /> 160 label="Print the header from the A file prior to results" />
156 </xml> 161 </xml>
157 <!-- TODO this is currently not used, but we should make use of it --> 162 <!-- TODO this is currently not used, but we should make use of it -->
158 <xml name="genome_validator"> 163 <xml name="genome_validator">
159 <validator type="unspecified_build" /> 164 <validator type="unspecified_build" />
160 <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." /> 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." />
161 </xml> 166 </xml>
162 167
163 <!-- ToDo column_picker --> 168 <!-- ToDo column_picker -->
164 <xml name="choose_columns"> 169 <xml name="choose_columns">
165 <param name="cols" type="text" value="" 170 <param name="cols" argument="-c" type="text" value=""
166 label="Specify the column(s) that should be summarized" 171 label="Specify the column(s) that should be summarized"
167 help="comma separated (-c)"> 172 help="Comma separated">
168 <sanitizer invalid_char=""> 173 <sanitizer invalid_char="">
169 <valid initial="string.digits"><add value=","/></valid> 174 <valid initial="string.digits"><add value=","/></valid>
170 </sanitizer> 175 </sanitizer>
171 </param> 176 </param>
172 </xml> 177 </xml>
199 <yield /> 204 <yield />
200 </param> 205 </param>
201 </xml> 206 </xml>
202 207
203 <xml name="math_options"> 208 <xml name="math_options">
204 <option value="sum" selected="True">Sum - numeric only</option> 209 <option value="sum" selected="true">Sum - numeric only</option>
205 <option value="min">Min - numeric only</option> 210 <option value="min">Min - numeric only</option>
206 <option value="max">Max - numeric only</option> 211 <option value="max">Max - numeric only</option>
207 <option value="absmin">AbsMin - numeric only</option> 212 <option value="absmin">AbsMin - numeric only</option>
208 <option value="absmax">AbsMax - numeric only</option> 213 <option value="absmax">AbsMax - numeric only</option>
209 <option value="mean">Mean - numeric only</option> 214 <option value="mean">Mean - numeric only</option>