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comparison macros.xml @ 2:87eccfc7a11a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5725fea947162618d77de7b8011d18b2f16c7094
author iuc
date Sat, 21 Jan 2017 06:56:46 -0500
parents 67cf20fad4d2
children a3b7d002c6e8
comparison
equal deleted inserted replaced
1:67cf20fad4d2 2:87eccfc7a11a
19 </requirements> 19 </requirements>
20 </xml> 20 </xml>
21 <xml name="version_command"> 21 <xml name="version_command">
22 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command> 22 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
23 </xml> 23 </xml>
24 24
25 <xml name="citations"> 25 <xml name="citations">
26 <citations> 26 <citations>
27 <citation type="doi">10.1093/bioinformatics/btp352</citation> 27 <citation type="doi">10.1093/bioinformatics/btp352</citation>
28 <yield /> 28 <yield />
29 </citations> 29 </citations>
43 </xml> 43 </xml>
44 <token name="@PREPARE_INPUT_FILE@"> 44 <token name="@PREPARE_INPUT_FILE@">
45 <![CDATA[ 45 <![CDATA[
46 ## May need to symlink input if there is an associated 46 ## May need to symlink input if there is an associated
47 #set $input_vcf = 'input.vcf.gz' 47 #set $input_vcf = 'input.vcf.gz'
48 #if $input_file.datatype.file_ext == 'vcf' 48 #if $input_file.is_of_type('vcf')
49 bgzip -c "$input_file" > $input_vcf && 49 bgzip -c "$input_file" > $input_vcf &&
50 bcftools index $input_vcf && 50 bcftools index $input_vcf &&
51 #elif $input_file.datatype.file_ext == 'vcf_bgzip' 51 #elif $input_file.is_of_type('vcf_bgzip')
52 ln -s "$input_file" $input_vcf 52 ln -s "$input_file" $input_vcf
53 #elif $input_file.datatype.file_ext == 'bcf' 53 #elif $input_file.is_of_type('bcf')
54 #set $input_vcf = 'input.bcf' 54 #set $input_vcf = 'input.bcf'
55 ln -s "$input_file" $input_vcf && 55 ln -s "$input_file" $input_vcf &&
56 #if $input_file.metadata.bcf_index: 56 #if $input_file.metadata.bcf_index:
57 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && 57 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
58 #else 58 #else
59 bcftools index $input_vcf && 59 bcftools index $input_vcf &&
60 #end if 60 #end if
61 #elif $input_file.datatype.file_ext == 'bcf_bgzip' 61 #elif $input_file.is_of_type('bcf_bgzip')
62 ln -s "$input_file" $input_vcf 62 ln -s "$input_file" $input_vcf
63 #end if 63 #end if
64 ]]> 64 ]]>
65 </token> 65 </token>
66 <token name="@INPUT_FILE@"> 66 <token name="@INPUT_FILE@">
75 ## May need to symlink input if there is an associated 75 ## May need to symlink input if there is an associated
76 #set $input_vcfs = [] 76 #set $input_vcfs = []
77 #set $vcfs_list_file = 'vcfs_list' 77 #set $vcfs_list_file = 'vcfs_list'
78 #for (i,input_file) in enumerate($input_files): 78 #for (i,input_file) in enumerate($input_files):
79 #set $input_vcf = 'input' + str($i) + '.vcf.gz' 79 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
80 #if $input_file.datatype.file_ext == 'vcf' 80 #if $input_file.is_of_type('vcf')
81 bgzip -c "$input_file" > $input_vcf && 81 bgzip -c "$input_file" > $input_vcf &&
82 bcftools index $input_vcf && 82 bcftools index $input_vcf &&
83 #elif $input_file.datatype.file_ext == 'vcf_bgz' 83 #elif $input_file.is_of_type('vcf_bgz')
84 ln -s "$input_file" $input_vcf 84 ln -s "$input_file" $input_vcf
85 #elif $input_file.datatype.file_ext == 'bcf' 85 #elif $input_file.is_of_type('bcf')
86 #set $input_vcf = 'input' + str($i) + '.bcf.gz' 86 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
87 ## bgzip -c "$input_file" > $input_vcf && 87 ## bgzip -c "$input_file" > $input_vcf &&
88 ln -s "$input_file" $input_vcf && 88 ln -s "$input_file" $input_vcf &&
89 #if $input_file.metadata.bcf_index: 89 #if $input_file.metadata.bcf_index:
90 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && 90 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
91 #else 91 #else
92 bcftools index $input_vcf && 92 bcftools index $input_vcf &&
93 #end if 93 #end if
94 #elif $input_file.datatype.file_ext == 'bcfvcf_bgz' 94 #elif $input_file.is_of_type('bcfvcf_bgz')
95 ln -s "$input_file" $input_vcf && 95 ln -s "$input_file" $input_vcf &&
96 #end if 96 #end if
97 echo '$input_vcf' >> $vcfs_list_file && 97 echo '$input_vcf' >> $vcfs_list_file &&
98 $input_vcfs.append($input_vcf) 98 $input_vcfs.append($input_vcf)
99 #end for 99 #end for
223 --collapse "${section.collapse}" 223 --collapse "${section.collapse}"
224 #end if 224 #end if
225 </token> 225 </token>
226 226
227 <xml name="macro_apply_filters"> 227 <xml name="macro_apply_filters">
228 <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true" 228 <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;)"> 229 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,]+)*)?$</validator> 230 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
231 </param> 231 </param>
232 </xml> 232 </xml>
233 <token name="@APPLY_FILTERS@"> 233 <token name="@APPLY_FILTERS@">
270 <option value="regions">regions</option> 270 <option value="regions">regions</option>
271 <option value="regions_file">regions-file</option> 271 <option value="regions_file">regions-file</option>
272 </param> 272 </param>
273 <when value="__none__"/> 273 <when value="__none__"/>
274 <when value="regions"> 274 <when value="regions">
275 <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true" 275 <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"> 276 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+)?)?)*)?$</validator> 277 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
278 </param> 278 </param>
279 </when> 279 </when>
280 <when value="regions_file"> 280 <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" /> 297 <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> 298 </xml>
299 <token name="@PREPARE_TARGETS_FILE@"> 299 <token name="@PREPARE_TARGETS_FILE@">
300 <![CDATA[ 300 <![CDATA[
301 #set $targets_path = None 301 #set $targets_path = None
302 #if 'targets' in $section 302 #if 'targets' in $section
303 #if $section.targets.targets_src == 'targets_file': 303 #if $section.targets.targets_src == 'targets_file':
304 #set $targets_path = 'targets_file.tab.gz' 304 #set $targets_path = 'targets_file.tab.gz'
305 bgzip -c "$section.targets.targets_file" > $targets_path && 305 bgzip -c "$section.targets.targets_file" > $targets_path &&
306 tabix -s 1 -b 2 -e 2 $targets_path && 306 tabix -s 1 -b 2 -e 2 $targets_path &&
307 #end if 307 #end if
329 <option value="targets">targets</option> 329 <option value="targets">targets</option>
330 <option value="targets_file">targets-file</option> 330 <option value="targets_file">targets-file</option>
331 </param> 331 </param>
332 <when value="__none__"/> 332 <when value="__none__"/>
333 <when value="targets"> 333 <when value="targets">
334 <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true" 334 <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true"
335 help="Each target is specifed as: chr or chr:pos or chr:from-to"> 335 help="Each target is specifed as: chr or chr:pos or chr:from-to">
336 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> 336 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
337 </param> 337 </param>
338 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" /> 338 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />
339 </when> 339 </when>
340 <when value="targets_file"> 340 <when value="targets_file">
341 <expand macro="macro_targets_file"> 341 <expand macro="macro_targets_file">
342 <optional>true</optional>
343 </expand> 342 </expand>
344 </when> 343 </when>
345 </conditional> 344 </conditional>
346 </xml> 345 </xml>
347 <token name="@TARGETS@"> 346 <token name="@TARGETS@">
357 #end if 356 #end if
358 ]]> 357 ]]>
359 </token> 358 </token>
360 359
361 <xml name="macro_samples"> 360 <xml name="macro_samples">
362 <param name="samples" type="text" value="" label="Samples" optional="true" 361 <param name="samples" type="text" value="" label="Samples" optional="true"
363 help="(-s) comma separated list of samples to annotate (or exclude with &quot;^&quot; prefix)"> 362 help="(-s) comma separated list of samples to annotate (or exclude with &quot;^&quot; prefix)">
364 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator> 363 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
365 </param> 364 </param>
366 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" 365 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
367 help="inverts the query/filtering applied by Samples" /> 366 help="inverts the query/filtering applied by Samples" />
368 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True" 367 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
369 help="(-S) file of samples to include" /> 368 help="(-S) file of samples to include" />
370 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File" 369 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"
371 help="inverts the query/filtering applied by Samples File" /> 370 help="inverts the query/filtering applied by Samples File" />
372 </xml> 371 </xml>
373 <token name="@SAMPLES@"> 372 <token name="@SAMPLES@">
374 #set $samples_defined = False 373 #set $samples_defined = False
375 #if str($section.samples) != '': 374 #if str($section.samples) != '':
415 --exclude '${section.exclude}' 414 --exclude '${section.exclude}'
416 #end if 415 #end if
417 </token> 416 </token>
418 417
419 <xml name="macro_columns"> 418 <xml name="macro_columns">
420 <param name="columns" type="text" value="" label="Columns" optional="true" 419 <param name="columns" type="text" value="" label="Columns" optional="true"
421 help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details"> 420 help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
422 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator> 421 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
423 </param> 422 </param>
424 </xml> 423 </xml>
425 <token name="@COLUMNS@"> 424 <token name="@COLUMNS@">
442 <token name="@OUTPUT_HELP@"> 441 <token name="@OUTPUT_HELP@">
443 <![CDATA[ 442 <![CDATA[
444 Output Type 443 Output Type
445 ----------- 444 -----------
446 445
447 Output compressed BCF (b), or uncompressed VCF (v). 446 Output compressed BCF (b), or uncompressed VCF (v).
448 Use the BCF option when piping between bcftools subcommands to speed up 447 Use the BCF option when piping between bcftools subcommands to speed up
449 performance by removing unecessary compression/decompression 448 performance by removing unecessary compression/decompression
450 and VCF<->BCF conversion. 449 and VCF<->BCF conversion.
451 450
452 This Galaxy tool recommends using the compressed BCF format 451 This Galaxy tool recommends using the compressed BCF format