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comparison macros.xml @ 7:6cbb9c47795c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author iuc
date Thu, 21 Feb 2019 15:55:43 -0500
parents 0594ea1417c8
children 2f8261ee0ea9
comparison
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6:0594ea1417c8 7:6cbb9c47795c
1 <macros> 1 <macros>
2 <token name="@VERSION@">1.4.0</token> 2 <token name="@TOOL_VERSION@">1.9</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="1.4">bcftools</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
14 <requirement type="package" version="1.4">htslib</requirement> 14 <requirement type="package" version="1.9">htslib</requirement>
15 <yield /> 15 <yield />
16 </requirements> 16 </requirements>
17 </xml> 17 </xml>
18 <xml name="samtools_requirement"> 18 <xml name="samtools_requirement">
19 <requirement type="package" version="1.3.1">samtools</requirement> 19 <requirement type="package" version="1.9">samtools</requirement>
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
37 <![CDATA[ 37 <![CDATA[
38 export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; 38 export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;
39 ]]> 39 ]]>
40 </token> 40 </token>
41 <xml name="macro_input"> 41 <xml name="macro_input">
42 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" /> 42 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
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.is_of_type('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.is_of_type('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 #if $input_file.metadata.tabix_index:
54 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
55 #else
56 bcftools index $input_vcf &&
57 #end if
53 #elif $input_file.is_of_type('bcf') 58 #elif $input_file.is_of_type('bcf')
54 #set $input_vcf = 'input.bcf' 59 #set $input_vcf = 'input.bcf'
55 ln -s '$input_file' $input_vcf && 60 ln -s '$input_file' $input_vcf &&
56 #if $input_file.metadata.bcf_index: 61 #if $input_file.metadata.bcf_index:
57 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi && 62 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
58 #else 63 #else
59 bcftools index $input_vcf && 64 bcftools index $input_vcf &&
60 #end if 65 #end if
61 #elif $input_file.is_of_type('bcf_bgzip')
62 ln -s '$input_file' $input_vcf &&
63 #end if 66 #end if
64 ]]> 67 ]]>
65 </token> 68 </token>
66 <token name="@INPUT_FILE@"> 69 <token name="@INPUT_FILE@">
67 $input_vcf 70 $input_vcf
68 </token> 71 </token>
69 72
70 <xml name="macro_inputs"> 73 <xml name="macro_inputs">
71 <param name="input_files" type="data" format="vcf,bcf" label="Other VCF/BCF Datasets" multiple="True" /> 74 <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
72 </xml> 75 </xml>
73 <token name="@PREPARE_INPUT_FILES@"> 76 <token name="@PREPARE_INPUT_FILES@">
74 <![CDATA[ 77 <![CDATA[
75 ## May need to symlink input if there is an associated 78 ## May need to symlink input if there is an associated
76 #set $input_vcfs = [] 79 #set $input_vcfs = []
78 #for (i, input_file) in enumerate($input_files): 81 #for (i, input_file) in enumerate($input_files):
79 #set $input_vcf = 'input' + str($i) + '.vcf.gz' 82 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
80 #if $input_file.is_of_type('vcf') 83 #if $input_file.is_of_type('vcf')
81 bgzip -c '$input_file' > $input_vcf && 84 bgzip -c '$input_file' > $input_vcf &&
82 bcftools index $input_vcf && 85 bcftools index $input_vcf &&
83 #elif $input_file.is_of_type('vcf_bgz') 86 #elif $input_file.is_of_type('vcf_bgzip')
84 ln -s '$input_file' $input_vcf 87 ln -s '$input_file' $input_vcf &&
88 #if $input_file.metadata.tabix_index:
89 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
90 #else
91 bcftools index $input_vcf &&
92 #end if
85 #elif $input_file.is_of_type('bcf') 93 #elif $input_file.is_of_type('bcf')
86 #set $input_vcf = 'input' + str($i) + '.bcf.gz' 94 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
87 ln -s '$input_file' $input_vcf && 95 ln -s '$input_file' $input_vcf &&
88 #if $input_file.metadata.bcf_index: 96 #if $input_file.metadata.bcf_index:
89 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi && 97 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
90 #else 98 #else
91 bcftools index $input_vcf && 99 bcftools index $input_vcf &&
92 #end if 100 #end if
93 #elif $input_file.is_of_type('bcfvcf_bgz')
94 ln -s '$input_file' $input_vcf &&
95 #end if 101 #end if
96 echo '$input_vcf' >> $vcfs_list_file && 102 echo '$input_vcf' >> $vcfs_list_file &&
97 $input_vcfs.append($input_vcf) 103 $input_vcfs.append($input_vcf)
98 #end for 104 #end for
99 ]]> 105 ]]>
104 <token name="@INPUT_LIST_FILE@"> 110 <token name="@INPUT_LIST_FILE@">
105 $vcfs_list_file 111 $vcfs_list_file
106 </token> 112 </token>
107 113
108 <xml name="macro_fasta_ref"> 114 <xml name="macro_fasta_ref">
109 <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" label="Reference sequence in FASTA format" optional="True" /> 115 <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" optional="true" label="Reference sequence in FASTA format" />
110 </xml> 116 </xml>
111 <token name="@PREPARE_FASTA_REF@"> 117 <token name="@PREPARE_FASTA_REF@">
112 <![CDATA[ 118 <![CDATA[
113 #set $input_fa_ref = None 119 #set $input_fa_ref = None
114 #if 'fasta_ref' in $section and $section.fasta_ref: 120 #if 'fasta_ref' in $section and $section.fasta_ref:
146 </conditional> 152 </conditional>
147 </xml> 153 </xml>
148 154
149 155
150 <xml name="macro_AF_file"> 156 <xml name="macro_AF_file">
151 <param name="AF_file" argument="--AF-file" type="data" format="tabular" label="Allele frequencies file" optional="True" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" /> 157 <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
152 </xml> 158 </xml>
153 <!-- This may need to bgzip and tabix the file --> 159 <!-- This may need to bgzip and tabix the file -->
154 <token name="@PREPARE_AF_FILE@"> 160 <token name="@PREPARE_AF_FILE@">
155 <![CDATA[ 161 <![CDATA[
156 #if 'AF_file' in $section and $section.AF_file: 162 #if 'AF_file' in $section and $section.AF_file:
163 --AF-file '${section.AF_file}' 169 --AF-file '${section.AF_file}'
164 #end if 170 #end if
165 </token> 171 </token>
166 172
167 <xml name="macro_estimate_AF"> 173 <xml name="macro_estimate_AF">
168 <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" label="Estimate allele frequency" optional="True" help="calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" /> 174 <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
169 </xml> 175 </xml>
170 <token name="@ESTIMATE_AF@"> 176 <token name="@ESTIMATE_AF@">
171 #if 'estimate_AF' in $section and $section.estimate_AF: 177 #if 'estimate_AF' in $section and $section.estimate_AF:
172 --estimate-AF "${section.estimate_AF}" 178 --estimate-AF "${section.estimate_AF}"
173 #end if 179 #end if
174 </token> 180 </token>
175 181
176 <xml name="macro_exons_file"> 182 <xml name="macro_exons_file">
177 <param name="exons_file" type="data" format="tabular" label="exons file" optional="True" help="tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" /> 183 <param name="exons_file" type="data" format="tabular" optional="true" label="Exons file" help="Tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
178 </xml> 184 </xml>
179 <token name="@PREPARE_EXONS_FILE@"> 185 <token name="@PREPARE_EXONS_FILE@">
180 <![CDATA[ 186 <![CDATA[
181 #set $exons_path = None 187 #set $exons_path = None
182 #if 'exons_file' in $section and $section.exons_file: 188 #if 'exons_file' in $section and $section.exons_file:
191 --exons $exons_path 197 --exons $exons_path
192 #end if 198 #end if
193 </token> 199 </token>
194 200
195 <xml name="macro_ploidy_file"> 201 <xml name="macro_ploidy_file">
196 <param name="ploidy_file" type="data" format="tabular" label="Ploidy file" optional="True" help="tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" /> 202 <param name="ploidy_file" type="data" format="tabular" optional="true" label="Ploidy file" help="Tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
197 </xml> 203 </xml>
198 <token name="@PLOIDY_FILE@"> 204 <token name="@PLOIDY_FILE@">
199 #if 'ploidy_file' in $section and $section.ploidy_file: 205 #if 'ploidy_file' in $section and $section.ploidy_file:
200 --ploidy "${section.ploidy_file}" 206 --ploidy "${section.ploidy_file}"
201 #end if 207 #end if
206 </xml> 212 </xml>
207 <xml name="macro_collapse_opt_id"> 213 <xml name="macro_collapse_opt_id">
208 <option value="id">id - only records with identical ID column are compatible. </option> 214 <option value="id">id - only records with identical ID column are compatible. </option>
209 </xml> 215 </xml>
210 <xml name="macro_collapse"> 216 <xml name="macro_collapse">
211 <param name="collapse" type="select" label="Collapse" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files"> 217 <param name="collapse" type="select" optional="true" label="Collapse" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
212 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option> 218 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
213 <option value="indels">indels - allow different alleles, as long as they all are indels</option> 219 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
214 <option value="both">both - indels and snps </option> 220 <option value="both">both - indels and snps </option>
215 <option value="some">some - at least some of the ALTs must match</option> 221 <option value="some">some - at least some of the ALTs must match</option>
216 <option value="any">any - any combination of alleles</option> 222 <option value="any">any - any combination of alleles</option>
222 --collapse ${section.collapse} 228 --collapse ${section.collapse}
223 #end if 229 #end if
224 </token> 230 </token>
225 231
226 <xml name="macro_apply_filters"> 232 <xml name="macro_apply_filters">
227 <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true" 233 <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters"
228 help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)"> 234 help="Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
229 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator> 235 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
230 </param> 236 </param>
231 </xml> 237 </xml>
232 <token name="@APPLY_FILTERS@"> 238 <token name="@APPLY_FILTERS@">
233 #if $section.apply_filters: 239 #if $section.apply_filters:
269 <option value="regions">regions</option> 275 <option value="regions">regions</option>
270 <option value="regions_file">regions-file</option> 276 <option value="regions_file">regions-file</option>
271 </param> 277 </param>
272 <when value="__none__"/> 278 <when value="__none__"/>
273 <when value="regions"> 279 <when value="regions">
274 <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true" 280 <param name="regions" type="text" value="" optional="true" label="Restrict to comma-separated list of regions"
275 help="Each region is specifed as: chr or chr:pos or chr:from-to"> 281 help="Each region is specifed as: chr or chr:pos or chr:from-to">
276 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> 282 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
277 </param> 283 </param>
278 </when> 284 </when>
279 <when value="regions_file"> 285 <when value="regions_file">
280 <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" /> 286 <param name="regions_file" type="data" format="vcf,bed,tabular" optional="true" label="Regions file" help="Restrict to regions listed in a file" />
281 </when> 287 </when>
282 </conditional> 288 </conditional>
283 </xml> 289 </xml>
284 <token name="@PREPARE_REGIONS_FILE@"> 290 <token name="@PREPARE_REGIONS_FILE@">
285 <![CDATA[ 291 <![CDATA[
344 <option value="targets">targets</option> 350 <option value="targets">targets</option>
345 <option value="targets_file">targets-file</option> 351 <option value="targets_file">targets-file</option>
346 </param> 352 </param>
347 <when value="__none__"/> 353 <when value="__none__"/>
348 <when value="targets"> 354 <when value="targets">
349 <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true" 355 <param name="targets" type="text" value="" optional="true" label="Restrict to comma-separated list of targets"
350 help="Each target is specifed as: chr or chr:pos or chr:from-to"> 356 help="Each target is specifed as: chr or chr:pos or chr:from-to">
351 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> 357 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
352 </param> 358 </param>
353 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" /> 359 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />
354 </when> 360 </when>
371 #end if 377 #end if
372 ]]> 378 ]]>
373 </token> 379 </token>
374 380
375 <xml name="macro_samples"> 381 <xml name="macro_samples">
376 <param name="samples" type="text" value="" label="Samples" optional="true" 382 <param argument="--samples" type="text" value="" optional="true" label="Samples"
377 help="(-s) comma separated list of samples to annotate (or exclude)"> 383 help="Comma separated list of samples to annotate (or exclude)">
378 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator> 384 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
379 </param> 385 </param>
380 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" 386 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
381 help="inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" /> 387 help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
382 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True" 388 <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"
383 help="(-S) file of samples to include" /> 389 help="File of samples to include" />
384 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File" 390 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"
385 help="inverts the query/filtering applied by Samples File" /> 391 help="inverts the query/filtering applied by Samples file" />
386 </xml> 392 </xml>
387 <token name="@SAMPLES@"> 393 <token name="@SAMPLES@">
388 #set $samples_defined = False 394 #set $samples_defined = False
389 #if str($section.samples) != '': 395 #if str($section.samples) != '':
390 #set $samples_defined = True 396 #set $samples_defined = True
395 --samples-file "${section.invert_samples_file}${section.samples_file}" 401 --samples-file "${section.invert_samples_file}${section.samples_file}"
396 #end if 402 #end if
397 </token> 403 </token>
398 404
399 <xml name="macro_sample"> 405 <xml name="macro_sample">
400 <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" /> 406 <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
401 </xml> 407 </xml>
402 <token name="@SAMPLE@"> 408 <token name="@SAMPLE@">
403 #if $section.sample: 409 #if $section.sample:
404 --sample '${section.sample}' 410 --sample '${section.sample}'
405 #end if 411 #end if
406 </token> 412 </token>
407 413
408 414
409 <xml name="macro_include"> 415 <xml name="macro_include">
410 <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true"> 416 <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">
411 <validator type="regex" message="Single quote not allowed">^[^']*$</validator> 417 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
412 <sanitizer sanitize="False"/> 418 <sanitizer sanitize="False"/>
413 </param> 419 </param>
414 </xml> 420 </xml>
415 <token name="@INCLUDE@"> 421 <token name="@INCLUDE@">
417 --include '${section.include}' 423 --include '${section.include}'
418 #end if 424 #end if
419 </token> 425 </token>
420 426
421 <xml name="macro_exclude"> 427 <xml name="macro_exclude">
422 <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true"> 428 <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">
423 <validator type="regex" message="Single quote not allowed">^[^']*$</validator> 429 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
424 <sanitizer sanitize="False"/> 430 <sanitizer sanitize="False"/>
425 </param> 431 </param>
426 </xml> 432 </xml>
427 <token name="@EXCLUDE@"> 433 <token name="@EXCLUDE@">
429 --exclude '${section.exclude}' 435 --exclude '${section.exclude}'
430 #end if 436 #end if
431 </token> 437 </token>
432 438
433 <xml name="macro_columns"> 439 <xml name="macro_columns">
434 <param name="columns" type="text" value="" label="Columns" optional="true" 440 <param name="columns" type="text" value="" optional="true" label="Columns"
435 help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details"> 441 help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
436 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator> 442 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
437 </param> 443 </param>
438 </xml> 444 </xml>
439 <token name="@COLUMNS@"> 445 <token name="@COLUMNS@">
440 #if $section.columns != '': 446 #if $section.columns != '':