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comparison macros.xml @ 5:cfd95c205d55 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author iuc
date Thu, 13 Apr 2017 17:42:23 -0400
parents f06ccd8eb3f6
children 963a3635b2e1
comparison
equal deleted inserted replaced
4:f06ccd8eb3f6 5:cfd95c205d55
1 <macros> 1 <macros>
2 <token name="@VERSION@">1.3.1</token> 2 <token name="@VERSION@">1.4.0</token>
3 <xml name="stdio"> 3 <xml name="stdio">
4 <stdio> 4 <stdio>
5 <exit_code range="1:" /> 5 <exit_code range="1:" />
6 <exit_code range=":-1" /> 6 <exit_code range=":-1" />
7 <regex match="Error:" /> 7 <regex match="Error:" />
8 <regex match="Exception:" /> 8 <regex match="Exception:" />
9 </stdio> 9 </stdio>
10 </xml> 10 </xml>
11 <xml name="requirements"> 11 <xml name="requirements">
12 <requirements> 12 <requirements>
13 <requirement type="package" version="1.3.1">bcftools</requirement> 13 <requirement type="package" version="1.4">bcftools</requirement>
14 <!-- conda dependency --> 14 <requirement type="package" version="1.4">htslib</requirement>
15 <requirement type="package" version="1.3.2">htslib</requirement>
16 <yield /> 15 <yield />
17 </requirements> 16 </requirements>
17 </xml>
18 <xml name="samtools_requirement">
19 <requirement type="package" version="1.3.1">samtools</requirement>
18 </xml> 20 </xml>
19 <xml name="version_command"> 21 <xml name="version_command">
20 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command> 22 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
21 </xml> 23 </xml>
22 24
243 <option value="v">uncompressed VCF</option> 245 <option value="v">uncompressed VCF</option>
244 </param> 246 </param>
245 </xml> 247 </xml>
246 <token name="@OUTPUT_TYPE@"> 248 <token name="@OUTPUT_TYPE@">
247 #if str($output_type) != "__none__": 249 #if str($output_type) != "__none__":
248 --output-type "${output_type}" 250 --output-type '${output_type}'
249 #end if 251 #end if
250 </token> 252 </token>
251 253
252 <xml name="macro_vcf_output"> 254 <xml name="macro_vcf_output">
253 <data name="output_file" format="vcf"> 255 <data name="output_file" format="vcf">
277 <when value="regions_file"> 279 <when value="regions_file">
278 <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" /> 280 <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" />
279 </when> 281 </when>
280 </conditional> 282 </conditional>
281 </xml> 283 </xml>
284 <token name="@PREPARE_REGIONS_FILE@">
285 <![CDATA[
286 #set $regions_path = None
287 #if 'regions' in $section
288 #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
289 #if $section.regions.regions_file.ext.startswith('bed'):
290 #set $regions_path = 'regions_file.bed'
291 ln -s '$section.regions.regions_file' $regions_path &&
292 #end if
293 #end if
294 #end if
295 ]]>
296 </token>
282 <token name="@REGIONS@"> 297 <token name="@REGIONS@">
283 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '': 298 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
284 --regions '$section.regions.regions' 299 --regions '$section.regions.regions'
285 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: 300 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
286 --regions-file '$section.regions.regions_file' 301 #if $regions_path is not None:
287 #end if 302 --regions-file '$regions_path'
288 </token> 303 #else:
289 304 --regions-file '$section.regions.regions_file'
305 #end if
306 #end if
307 </token>
290 <xml name="macro_targets_file"> 308 <xml name="macro_targets_file">
291 <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" > 309 <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
292 <yield/> 310 <yield/>
293 </param> 311 </param>
294 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" /> 312 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />
354 ]]> 372 ]]>
355 </token> 373 </token>
356 374
357 <xml name="macro_samples"> 375 <xml name="macro_samples">
358 <param name="samples" type="text" value="" label="Samples" optional="true" 376 <param name="samples" type="text" value="" label="Samples" optional="true"
359 help="(-s) comma separated list of samples to annotate (or exclude with &quot;^&quot; prefix)"> 377 help="(-s) comma separated list of samples to annotate (or exclude)">
360 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator> 378 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
361 </param> 379 </param>
362 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" 380 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
363 help="inverts the query/filtering applied by Samples" /> 381 help="inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
364 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True" 382 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
365 help="(-S) file of samples to include" /> 383 help="(-S) file of samples to include" />
366 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File" 384 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"
367 help="inverts the query/filtering applied by Samples File" /> 385 help="inverts the query/filtering applied by Samples File" />
368 </xml> 386 </xml>