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comparison macros.xml @ 54:b06c53665eb6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
author iuc
date Tue, 23 Mar 2021 20:21:30 +0000
parents 73e3ca75370a
children 7a06bb42dbb1
comparison
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53:73e3ca75370a 54:b06c53665eb6
3 <requirements> 3 <requirements>
4 <requirement type="package" version="@TOOL_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="@TOOL_VERSION@">2.29.2</token> 8 <token name="@TOOL_VERSION@">2.30.0</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,encodepeak</token> 10 <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf,encodepeak</token>
11 <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token> 11 <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token>
12 <xml name="stdio"> 12 <xml name="stdio">
13 <stdio> 13 <stdio>
75 <when value="hist"> 75 <when value="hist">
76 <param name="genome" type="data" format="tabular" label="Genome file" /> 76 <param name="genome" type="data" format="tabular" label="Genome file" />
77 </when> 77 </when>
78 </conditional> 78 </conditional>
79 </xml> 79 </xml>
80 <xml name="input_optional_genome_file">
81 <conditional name="genome">
82 <param name="genome_choose" argument="-g" type="select"
83 label="Specify a genome file that defines the expected chromosome order in the input files." >
84 <option value="" selected="true">No</option>
85 <option value="-g">Yes</option>
86 </param>
87 <when value="-g">
88 <expand macro="input_conditional_genome_file" />
89 </when>
90 <when value="" />
91 </conditional>
92 </xml>
80 <token name="@GENOME_FILE@"> 93 <token name="@GENOME_FILE@">
81 #if $genome_file_opts.genome_file_opts_selector == "loc": 94 #if $genome_file_opts.genome_file_opts_selector == "loc":
82 '$genome_file_opts.genome.fields.len_path' 95 '$genome_file_opts.genome.fields.len_path'
83 #elif $genome_file_opts.genome_file_opts_selector == "hist": 96 #elif $genome_file_opts.genome_file_opts_selector == "hist":
84 '$genome_file_opts.genome' 97 '$genome_file_opts.genome'
221 <option value="count">Count - numeric or text</option> 234 <option value="count">Count - numeric or text</option>
222 <option value="count_disctinct">Count Distinct - numeric or text</option> 235 <option value="count_disctinct">Count Distinct - numeric or text</option>
223 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option> 236 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
224 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option> 237 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
225 </xml> 238 </xml>
239 <xml name="sorted">
240 <!-- -sorted -g -->
241 <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
242 label="For coordinate sorted input file the more efficient sweeping algorithm is enabled."/>
243 </xml>
244 <token name="@SORTED@">
245 <![CDATA[
246 $sorted
247 #if str($sorted) != '':
248 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
249 -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
250 #else if str($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'):
251 -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
252 #end if
253 #end if
254 ]]>
255 </token>
226 <token name="@REFERENCES@"> 256 <token name="@REFERENCES@">
227 <![CDATA[ 257 <![CDATA[
228 ------ 258 ------
229 259
230 This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_. 260 This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_.