Mercurial > repos > iuc > bcftools_convert_to_vcf

comparison macros.xml @ 3:d6e3d97e17f0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
author iuc
date Tue, 31 Jan 2017 12:42:27 -0500
parents 98d4a7bfec83
children 19167fd970a3
comparison
equal deleted inserted replaced
2:98d4a7bfec83 3:d6e3d97e17f0
12 <xml name="requirements"> 12 <xml name="requirements">
13 <requirements> 13 <requirements>
14 <requirement type="package" version="1.3">bcftools</requirement> 14 <requirement type="package" version="1.3">bcftools</requirement>
15 <!-- conda dependency --> 15 <!-- conda dependency -->
16 <requirement type="package" version="1.3">htslib</requirement> 16 <requirement type="package" version="1.3">htslib</requirement>
17 <!-- htslib provides tabix and bgzip
17 <requirement type="package" version="0.2.6">tabix</requirement> 18 <requirement type="package" version="0.2.6">tabix</requirement>
19 -->
18 <requirement type="package" version="1.2">samtools</requirement> 20 <requirement type="package" version="1.2">samtools</requirement>
19 </requirements> 21 </requirements>
20 </xml> 22 </xml>
21 <xml name="version_command"> 23 <xml name="version_command">
22 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command> 24 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
23 </xml> 25 </xml>
24 26
25 <xml name="citations"> 27 <xml name="citations">
26 <citations> 28 <citations>
27 <citation type="doi">10.1093/bioinformatics/btp352</citation> 29 <citation type="doi">10.1093/bioinformatics/btp352</citation>
28 <yield /> 30 <yield />
29 </citations> 31 </citations>
43 </xml> 45 </xml>
44 <token name="@PREPARE_INPUT_FILE@"> 46 <token name="@PREPARE_INPUT_FILE@">
45 <![CDATA[ 47 <![CDATA[
46 ## May need to symlink input if there is an associated 48 ## May need to symlink input if there is an associated
47 #set $input_vcf = 'input.vcf.gz' 49 #set $input_vcf = 'input.vcf.gz'
48 #if $input_file.datatype.file_ext == 'vcf' 50 #if $input_file.is_of_type('vcf')
49 bgzip -c "$input_file" > $input_vcf && 51 bgzip -c "$input_file" > $input_vcf &&
50 bcftools index $input_vcf && 52 bcftools index $input_vcf &&
51 #elif $input_file.datatype.file_ext == 'vcf_bgzip' 53 #elif $input_file.is_of_type('vcf_bgzip')
52 ln -s "$input_file" $input_vcf 54 ln -s "$input_file" $input_vcf
53 #elif $input_file.datatype.file_ext == 'bcf' 55 #elif $input_file.is_of_type('bcf')
54 #set $input_vcf = 'input.bcf' 56 #set $input_vcf = 'input.bcf'
55 ln -s "$input_file" $input_vcf && 57 ln -s "$input_file" $input_vcf &&
56 #if $input_file.metadata.bcf_index: 58 #if $input_file.metadata.bcf_index:
57 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && 59 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
58 #else 60 #else
59 bcftools index $input_vcf && 61 bcftools index $input_vcf &&
60 #end if 62 #end if
61 #elif $input_file.datatype.file_ext == 'bcf_bgzip' 63 #elif $input_file.is_of_type('bcf_bgzip')
62 ln -s "$input_file" $input_vcf 64 ln -s "$input_file" $input_vcf
63 #end if 65 #end if
64 ]]> 66 ]]>
65 </token> 67 </token>
66 <token name="@INPUT_FILE@"> 68 <token name="@INPUT_FILE@">
75 ## May need to symlink input if there is an associated 77 ## May need to symlink input if there is an associated
76 #set $input_vcfs = [] 78 #set $input_vcfs = []
77 #set $vcfs_list_file = 'vcfs_list' 79 #set $vcfs_list_file = 'vcfs_list'
78 #for (i,input_file) in enumerate($input_files): 80 #for (i,input_file) in enumerate($input_files):
79 #set $input_vcf = 'input' + str($i) + '.vcf.gz' 81 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
80 #if $input_file.datatype.file_ext == 'vcf' 82 #if $input_file.is_of_type('vcf')
81 bgzip -c "$input_file" > $input_vcf && 83 bgzip -c "$input_file" > $input_vcf &&
82 bcftools index $input_vcf && 84 bcftools index $input_vcf &&
83 #elif $input_file.datatype.file_ext == 'vcf_bgz' 85 #elif $input_file.is_of_type('vcf_bgz')
84 ln -s "$input_file" $input_vcf 86 ln -s "$input_file" $input_vcf
85 #elif $input_file.datatype.file_ext == 'bcf' 87 #elif $input_file.is_of_type('bcf')
86 #set $input_vcf = 'input' + str($i) + '.bcf.gz' 88 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
87 ## bgzip -c "$input_file" > $input_vcf && 89 ## bgzip -c "$input_file" > $input_vcf &&
88 ln -s "$input_file" $input_vcf && 90 ln -s "$input_file" $input_vcf &&
89 #if $input_file.metadata.bcf_index: 91 #if $input_file.metadata.bcf_index:
90 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && 92 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
91 #else 93 #else
92 bcftools index $input_vcf && 94 bcftools index $input_vcf &&
93 #end if 95 #end if
94 #elif $input_file.datatype.file_ext == 'bcfvcf_bgz' 96 #elif $input_file.is_of_type('bcfvcf_bgz')
95 ln -s "$input_file" $input_vcf && 97 ln -s "$input_file" $input_vcf &&
96 #end if 98 #end if
97 echo '$input_vcf' >> $vcfs_list_file && 99 echo '$input_vcf' >> $vcfs_list_file &&
98 $input_vcfs.append($input_vcf) 100 $input_vcfs.append($input_vcf)
99 #end for 101 #end for
223 --collapse "${section.collapse}" 225 --collapse "${section.collapse}"
224 #end if 226 #end if
225 </token> 227 </token>
226 228
227 <xml name="macro_apply_filters"> 229 <xml name="macro_apply_filters">
228 <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true" 230 <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true"
229 help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)"> 231 help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
230 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator> 232 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
231 </param> 233 </param>
232 </xml> 234 </xml>
233 <token name="@APPLY_FILTERS@"> 235 <token name="@APPLY_FILTERS@">
270 <option value="regions">regions</option> 272 <option value="regions">regions</option>
271 <option value="regions_file">regions-file</option> 273 <option value="regions_file">regions-file</option>
272 </param> 274 </param>
273 <when value="__none__"/> 275 <when value="__none__"/>
274 <when value="regions"> 276 <when value="regions">
275 <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true" 277 <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true"
276 help="Each region is specifed as: chr or chr:pos or chr:from-to"> 278 help="Each region is specifed as: chr or chr:pos or chr:from-to">
277 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> 279 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
278 </param> 280 </param>
279 </when> 281 </when>
280 <when value="regions_file"> 282 <when value="regions_file">
297 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" /> 299 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />
298 </xml> 300 </xml>
299 <token name="@PREPARE_TARGETS_FILE@"> 301 <token name="@PREPARE_TARGETS_FILE@">
300 <![CDATA[ 302 <![CDATA[
301 #set $targets_path = None 303 #set $targets_path = None
302 #if 'targets' in $section 304 #if 'targets' in $section
303 #if $section.targets.targets_src == 'targets_file': 305 #if $section.targets.targets_src == 'targets_file':
304 #set $targets_path = 'targets_file.tab.gz' 306 #set $targets_path = 'targets_file.tab.gz'
305 bgzip -c "$section.targets.targets_file" > $targets_path && 307 bgzip -c "$section.targets.targets_file" > $targets_path &&
306 tabix -s 1 -b 2 -e 2 $targets_path && 308 tabix -s 1 -b 2 -e 2 $targets_path &&
307 #end if 309 #end if
329 <option value="targets">targets</option> 331 <option value="targets">targets</option>
330 <option value="targets_file">targets-file</option> 332 <option value="targets_file">targets-file</option>
331 </param> 333 </param>
332 <when value="__none__"/> 334 <when value="__none__"/>
333 <when value="targets"> 335 <when value="targets">
334 <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true" 336 <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true"
335 help="Each target is specifed as: chr or chr:pos or chr:from-to"> 337 help="Each target is specifed as: chr or chr:pos or chr:from-to">
336 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> 338 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
337 </param> 339 </param>
338 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" /> 340 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />
339 </when> 341 </when>
356 #end if 358 #end if
357 ]]> 359 ]]>
358 </token> 360 </token>
359 361
360 <xml name="macro_samples"> 362 <xml name="macro_samples">
361 <param name="samples" type="text" value="" label="Samples" optional="true" 363 <param name="samples" type="text" value="" label="Samples" optional="true"
362 help="(-s) comma separated list of samples to annotate (or exclude with &quot;^&quot; prefix)"> 364 help="(-s) comma separated list of samples to annotate (or exclude with &quot;^&quot; prefix)">
363 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator> 365 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
364 </param> 366 </param>
365 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" 367 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
366 help="inverts the query/filtering applied by Samples" /> 368 help="inverts the query/filtering applied by Samples" />
367 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True" 369 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
368 help="(-S) file of samples to include" /> 370 help="(-S) file of samples to include" />
369 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File" 371 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"
370 help="inverts the query/filtering applied by Samples File" /> 372 help="inverts the query/filtering applied by Samples File" />
371 </xml> 373 </xml>
372 <token name="@SAMPLES@"> 374 <token name="@SAMPLES@">
373 #set $samples_defined = False 375 #set $samples_defined = False
374 #if str($section.samples) != '': 376 #if str($section.samples) != '':
414 --exclude '${section.exclude}' 416 --exclude '${section.exclude}'
415 #end if 417 #end if
416 </token> 418 </token>
417 419
418 <xml name="macro_columns"> 420 <xml name="macro_columns">
419 <param name="columns" type="text" value="" label="Columns" optional="true" 421 <param name="columns" type="text" value="" label="Columns" optional="true"
420 help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details"> 422 help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
421 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator> 423 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
422 </param> 424 </param>
423 </xml> 425 </xml>
424 <token name="@COLUMNS@"> 426 <token name="@COLUMNS@">
441 <token name="@OUTPUT_HELP@"> 443 <token name="@OUTPUT_HELP@">
442 <![CDATA[ 444 <![CDATA[
443 Output Type 445 Output Type
444 ----------- 446 -----------
445 447
446 Output compressed BCF (b), or uncompressed VCF (v). 448 Output compressed BCF (b), or uncompressed VCF (v).
447 Use the BCF option when piping between bcftools subcommands to speed up 449 Use the BCF option when piping between bcftools subcommands to speed up
448 performance by removing unecessary compression/decompression 450 performance by removing unecessary compression/decompression
449 and VCF<->BCF conversion. 451 and VCF<->BCF conversion.
450 452
451 This Galaxy tool recommends using the compressed BCF format 453 This Galaxy tool recommends using the compressed BCF format