Mercurial > repos > iuc > bcftools_convert_from_vcf

comparison macros.xml @ 16:9b29129fb491 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 12:56:02 +0000
parents 7cea7c7bf203
children b14ff40958cb
comparison
equal deleted inserted replaced
15:1137ce8efc1e 16:9b29129fb491
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.10</token> 2 <token name="@TOOL_VERSION@">1.15.1</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">20.01</token>
3 <xml name="bio_tools"> 5 <xml name="bio_tools">
4 <xrefs> 6 <xrefs>
5 <xref type="bio.tools">bcftools</xref> 7 <xref type="bio.tools">bcftools</xref>
6 </xrefs> 8 </xrefs>
7 </xml> 9 </xml>
8 <xml name="requirements"> 10 <xml name="requirements">
9 <requirements> 11 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement> 12 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
11 <requirement type="package" version="1.10">htslib</requirement> 13 <requirement type="package" version="1.15.1">htslib</requirement>
12 <yield /> 14 <yield />
13 </requirements> 15 </requirements>
14 </xml> 16 </xml>
15 <xml name="samtools_requirement"> 17 <xml name="samtools_requirement">
16 <requirement type="package" version="1.10">samtools</requirement> 18 <requirement type="package" version="1.15.1">samtools</requirement>
17 </xml> 19 </xml>
18 <xml name="matplotlib_requirement"> 20 <xml name="matplotlib_requirement">
19 <requirement type="package" version="3.4.3">matplotlib</requirement> 21 <requirement type="package" version="3.5.3">matplotlib</requirement>
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
37 <![CDATA[ 39 <![CDATA[
38 export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; 40 export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;
39 ]]> 41 ]]>
40 </token> 42 </token>
41 <xml name="macro_input"> 43 <xml name="macro_input">
44 <!--
45 REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files
46 <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
47 -->
42 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" /> 48 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
43 </xml> 49 </xml>
44 <token name="@PREPARE_INPUT_FILE@"> 50 <token name="@PREPARE_INPUT_FILE@">
45 <![CDATA[ 51 <![CDATA[
46 ## May need to symlink input if there is an associated 52 ## May need to symlink input if there is an associated
47 #set $input_vcf = 'input.vcf.gz' 53 #set $input_vcf = 'input.vcf.gz'
48 #if $input_file.is_of_type('vcf') 54 #if $input_file.is_of_type('vcf')
49 bgzip -c '$input_file' > $input_vcf && 55 bgzip -c '$input_file' > $input_vcf &&
50 bcftools index $input_vcf && 56 bcftools index $input_vcf &&
57 ##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
51 #elif $input_file.is_of_type('vcf_bgzip') 58 #elif $input_file.is_of_type('vcf_bgzip')
52 ln -s '$input_file' $input_vcf && 59 ln -s '$input_file' $input_vcf &&
53 #if $input_file.metadata.tabix_index: 60 #if $input_file.metadata.tabix_index:
54 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi && 61 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
55 #else 62 #else
69 <token name="@INPUT_FILE@"> 76 <token name="@INPUT_FILE@">
70 $input_vcf 77 $input_vcf
71 </token> 78 </token>
72 79
73 <xml name="macro_inputs"> 80 <xml name="macro_inputs">
81 <!--
82 REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files
83 <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
84 -->
74 <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" /> 85 <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
75 </xml> 86 </xml>
76 <token name="@PREPARE_INPUT_FILES@"> 87 <token name="@PREPARE_INPUT_FILES@">
77 <![CDATA[ 88 <![CDATA[
78 ## May need to symlink input if there is an associated 89 ## May need to symlink input if there is an associated
81 #for (i, input_file) in enumerate($input_files): 92 #for (i, input_file) in enumerate($input_files):
82 #set $input_vcf = 'input' + str($i) + '.vcf.gz' 93 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
83 #if $input_file.is_of_type('vcf') 94 #if $input_file.is_of_type('vcf')
84 bgzip -c '$input_file' > $input_vcf && 95 bgzip -c '$input_file' > $input_vcf &&
85 bcftools index $input_vcf && 96 bcftools index $input_vcf &&
86 #elif $input_file.is_of_type('vcf_bgzip') 97 ##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz') -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605
98 #elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
87 ln -s '$input_file' $input_vcf && 99 ln -s '$input_file' $input_vcf &&
88 #if $input_file.metadata.tabix_index: 100 #if $input_file.metadata.tabix_index:
89 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi && 101 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
90 #else 102 #else
91 bcftools index $input_vcf && 103 bcftools index $input_vcf &&
316 <when value="@TYPE@s_file"> 328 <when value="@TYPE@s_file">
317 <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" /> 329 <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
318 <yield /> 330 <yield />
319 </when> 331 </when>
320 </conditional> 332 </conditional>
333 <param argument="--@TYPE@s-overlap" type="select" optional="true" label="@LABEL_TYPE@ overlap" help="Include if POS in the region (0), record overlaps (1), variant overlaps (2)">
334 <option value="0">0: POS in the region</option>
335 <option value="1">1: Record overlaps</option>
336 <option value="2">2: Variant overlaps</option>
337 </param>
321 </xml> 338 </xml>
322 339
323 <token name="@PARSE_INTERVALS@"> 340 <token name="@PARSE_INTERVALS@">
324 <![CDATA[ 341 <![CDATA[
325 #set $components = [] 342 #set $components = []
335 #end for 352 #end for
336 #set $intervals_spec = ','.join($components) 353 #set $intervals_spec = ','.join($components)
337 ]]> 354 ]]>
338 </token> 355 </token>
339 356
357 <token name="@MASK@">
358 <![CDATA[
359 #if $section.conditional_soft_filter.selector == 'enabled' and $section.conditional_soft_filter.soft_filter
360 #if $section.conditional_soft_filter.masks.masks_src == 'regions':
361 #set $intervals = $section.conditional_soft_filter.masks.masks
362 @PARSE_INTERVALS@
363 --mask '$intervals_spec'
364 #elif $section.conditional_soft_filter.masks.masks_src == 'masks_file' and $section.conditional_soft_filter.masks.masks_file:
365 #if $masks_path is not None:
366 --mask-file '$masks_path'
367 #else:
368 --mask-file '$section.conditional_soft_filter.masks.masks_file'
369 #end if
370 #end if
371 #if $section.conditional_soft_filter.masks_overlap
372 --mask-overlap $section.conditional_soft_filter.masks_overlap
373 #end if
374 #end if
375
376 ]]>
377 </token>
378
340 <token name="@REGIONS@"> 379 <token name="@REGIONS@">
341 <![CDATA[ 380 <![CDATA[
342 #if $section.regions.regions_src == 'regions': 381 #if $section.regions.regions_src == 'regions':
343 #set $intervals = $section.regions.regions 382 #set $intervals = $section.regions.regions
344 @PARSE_INTERVALS@ 383 @PARSE_INTERVALS@
348 --regions-file '$regions_path' 387 --regions-file '$regions_path'
349 #else: 388 #else:
350 --regions-file '$section.regions.regions_file' 389 --regions-file '$section.regions.regions_file'
351 #end if 390 #end if
352 #end if 391 #end if
392 #if $section.regions_overlap
393 --regions-overlap $section.regions_overlap
394 #end if
395
353 ]]> 396 ]]>
354 </token> 397 </token>
355 398
356 <token name="@TARGETS@"> 399 <token name="@TARGETS@">
357 <![CDATA[ 400 <![CDATA[
362 @PARSE_INTERVALS@ 405 @PARSE_INTERVALS@
363 --targets '${section.targets.invert_targets_file}$intervals_spec' 406 --targets '${section.targets.invert_targets_file}$intervals_spec'
364 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file: 407 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
365 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}" 408 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
366 #end if 409 #end if
410 #if $section.targets_overlap
411 --targets-overlap $section.targets_overlap
412 #end if
367 ]]> 413 ]]>
368 </token> 414 </token>
369 415
370 <token name="@PREPARE_REGIONS_FILE@"> 416 <token name="@PREPARE_REGIONS_FILE@">
371 <![CDATA[ 417 <![CDATA[
408 ]]> 454 ]]>
409 </token> 455 </token>
410 456
411 <xml name="macro_samples"> 457 <xml name="macro_samples">
412 <param argument="--samples" type="text" value="" optional="true" label="Samples" 458 <param argument="--samples" type="text" value="" optional="true" label="Samples"
413 help="Comma separated list of samples to annotate (or exclude)"> 459 help="Comma-separated list of samples to annotate (or exclude) or - to include all samples">
414 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator> 460 <validator type="regex" message="Comma-separated list of samples or - to include all samples">^(-|\w+(,\w+)*)?$</validator>
415 </param> 461 </param>
416 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" 462 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
417 help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" /> 463 help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
418 <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file" 464 <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"
419 help="File of samples to include" /> 465 help="File of samples to include" />
474 </token> 520 </token>
475 521
476 <xml name="macro_columns"> 522 <xml name="macro_columns">
477 <param name="columns" type="text" value="" optional="true" label="Columns" 523 <param name="columns" type="text" value="" optional="true" label="Columns"
478 help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details"> 524 help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
479 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator> 525 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
480 </param> 526 </param>
481 </xml> 527 </xml>
482 <token name="@COLUMNS@"> 528 <token name="@COLUMNS@">
483 #if $section.columns != '': 529 #if $section.columns != '':
484 --columns '${section.columns}' 530 --columns '${section.columns}'
494 </xml> 540 </xml>
495 <token name="@VCF_IDS@"> 541 <token name="@VCF_IDS@">
496 ${section.vcf_ids} 542 ${section.vcf_ids}
497 </token> 543 </token>
498 544
545 <xml name="macro_output_tags">
546 <param name="output_tags" argument="--annotate" type="select" optional="true" multiple="True" display="checkboxes" label="Optional tags to output" help="--annotate">
547 <yield />
548 </param>
549 </xml>
550
551 <xml name="macro_overlap" token_argument="" token_label="">
552 </xml>
553
554
499 <token name="@OUTPUT_HELP@"> 555 <token name="@OUTPUT_HELP@">
556
500 <![CDATA[ 557 <![CDATA[
501 Output Type 558 Output Type
502 ----------- 559 -----------
503 560
504 Output compressed BCF (b), or uncompressed VCF (v). 561 Output compressed BCF (b), or uncompressed VCF (v).