Mercurial > repos > iuc > bcftools_plugin_impute_info
comparison macros.xml @ 8:9b298d4d10c2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author | iuc |
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date | Wed, 05 Jun 2019 13:16:01 -0400 |
parents | 6f8e223f78f3 |
children | 0c1889b0917b |
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7:6f8e223f78f3 | 8:9b298d4d10c2 |
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1 <macros> | 1 <macros> |
2 <token name="@TOOL_VERSION@">1.9</token> | 2 <token name="@TOOL_VERSION@">1.9</token> |
3 <xml name="stdio"> | |
4 <stdio> | |
5 <exit_code range="1:" /> | |
6 <exit_code range=":-1" /> | |
7 <regex match="Error:" /> | |
8 <regex match="Exception:" /> | |
9 </stdio> | |
10 </xml> | |
11 <xml name="requirements"> | 3 <xml name="requirements"> |
12 <requirements> | 4 <requirements> |
13 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement> | 5 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement> |
14 <requirement type="package" version="1.9">htslib</requirement> | 6 <requirement type="package" version="1.9">htslib</requirement> |
15 <yield /> | 7 <yield /> |
16 </requirements> | 8 </requirements> |
17 </xml> | 9 </xml> |
18 <xml name="samtools_requirement"> | 10 <xml name="samtools_requirement"> |
19 <requirement type="package" version="1.9">samtools</requirement> | 11 <requirement type="package" version="1.9">samtools</requirement> |
12 </xml> | |
13 <xml name="matplotlib_requirement"> | |
14 <requirement type="package" version="3.1.0">matplotlib</requirement> | |
20 </xml> | 15 </xml> |
21 <xml name="version_command"> | 16 <xml name="version_command"> |
22 <version_command>bcftools 2>&1 | grep 'Version:'</version_command> | 17 <version_command>bcftools 2>&1 | grep 'Version:'</version_command> |
23 </xml> | 18 </xml> |
24 | 19 |
109 </token> | 104 </token> |
110 <token name="@INPUT_LIST_FILE@"> | 105 <token name="@INPUT_LIST_FILE@"> |
111 $vcfs_list_file | 106 $vcfs_list_file |
112 </token> | 107 </token> |
113 | 108 |
109 <xml name="test_using_reference" token_select_from="history" token_ref=""> | |
110 <conditional name="reference_source"> | |
111 <param name="reference_source_selector" value="@SELECT_FROM@" /> | |
112 <param name="fasta_ref" ftype="fasta" value="@REF@" /> | |
113 </conditional> | |
114 </xml> | |
115 | |
114 <xml name="macro_fasta_ref"> | 116 <xml name="macro_fasta_ref"> |
115 <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" optional="true" label="Reference sequence in FASTA format" /> | 117 <conditional name="reference_source"> |
118 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
119 <option value="cached">Use a built-in genome</option> | |
120 <option value="history">Use a genome from the history</option> | |
121 </param> | |
122 <when value="cached"> | |
123 <param name="fasta_ref" type="select" label="Reference genome"> | |
124 <options from_data_table="fasta_indexes"> | |
125 <filter type="data_meta" column="1" key="dbkey" ref="input_file" /> | |
126 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> | |
127 </options> | |
128 </param> | |
129 </when> | |
130 <when value="history"> | |
131 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" /> | |
132 </when> | |
133 </conditional> | |
116 </xml> | 134 </xml> |
117 <token name="@PREPARE_FASTA_REF@"> | 135 <token name="@PREPARE_FASTA_REF@"> |
118 <![CDATA[ | 136 <![CDATA[ |
119 #set $input_fa_ref = None | 137 #set $input_fa_ref = None |
120 #if 'fasta_ref' in $section and $section.fasta_ref: | 138 #if 'fasta_ref' in $section and $section.fasta_ref: |
121 #set $input_fa_ref = 'ref.fa' | 139 #if 'reference_source_selector' in $section: |
122 ln -s '$section.fasta_ref' $input_fa_ref && | 140 #if str($section.reference_source_selector) == "history": |
123 samtools faidx $input_fa_ref && | 141 #set $input_fa_ref = 'ref.fa' |
142 ln -s '$section.fasta_ref' $input_fa_ref && | |
143 samtools faidx $input_fa_ref && | |
144 #else: | |
145 #set $input_fa_ref = str($section.fasta_ref.fields.path) | |
146 #end if | |
147 #end if | |
124 #end if | 148 #end if |
125 ]]> | 149 ]]> |
126 </token> | 150 </token> |
127 <token name="@FASTA_REF@"> | 151 <token name="@FASTA_REF@"> |
128 #if $input_fa_ref is not None: | 152 #if $input_fa_ref is not None: |
129 --fasta-ref $input_fa_ref | 153 --fasta-ref $input_fa_ref |
130 #elif 'fasta_ref' in $section and $section.fasta_ref: | 154 #elif 'fasta_ref' in $section and $section.fasta_ref: |
131 --fasta-ref '${section.fasta_ref}' | 155 --fasta-ref '${section.fasta_ref}' |
132 #end if | 156 #end if |
133 </token> | 157 </token> |
134 | |
135 <xml name="macro_ref_fasta"> | |
136 <conditional name="reference_source"> | |
137 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
138 <option value="cached">Locally cached</option> | |
139 <option value="history">History</option> | |
140 </param> | |
141 <when value="cached"> | |
142 <param name="ref_file" type="select" label="Select reference genome"> | |
143 <options from_data_table="fasta_indexes"> | |
144 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> | |
145 </options> | |
146 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
147 </param> | |
148 </when> | |
149 <when value="history"> <!-- FIX ME!!!! --> | |
150 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
151 </when> | |
152 </conditional> | |
153 </xml> | |
154 | |
155 | 158 |
156 <xml name="macro_AF_file"> | 159 <xml name="macro_AF_file"> |
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" /> | 160 <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" /> |
158 </xml> | 161 </xml> |
159 <!-- This may need to bgzip and tabix the file --> | 162 <!-- This may need to bgzip and tabix the file --> |
266 <when input="output_type" value="v" format="vcf" /> | 269 <when input="output_type" value="v" format="vcf" /> |
267 </change_format> | 270 </change_format> |
268 </data> | 271 </data> |
269 </xml> | 272 </xml> |
270 | 273 |
271 <xml name="macro_regions"> | 274 <xml name="macro_invert_targets"> |
272 <conditional name="regions"> | 275 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" |
273 <param name="regions_src" type="select" label="Regions"> | 276 label="Invert Targets" |
274 <option value="__none__">None</option> | 277 help="inverts the query/filtering applied by the targets" /> |
275 <option value="regions">regions</option> | 278 </xml> |
276 <option value="regions_file">regions-file</option> | 279 |
280 <xml name="macro_restriction_spec" token_type="region" token_label_type="Region"> | |
281 <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1"> | |
282 <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome"> | |
283 <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator> | |
284 </param> | |
285 <param name="start" type="text" label="@LABEL_TYPE@ start position"> | |
286 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> | |
287 </param> | |
288 <param name="stop" type="text" label="@LABEL_TYPE@ end position"> | |
289 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> | |
290 </param> | |
291 <yield /> | |
292 </repeat> | |
293 </xml> | |
294 | |
295 <xml name="macro_restrictions_file" token_type="region" token_label_type="Region"> | |
296 <param name="@TYPE@s_file" type="data" format="tabular" label="@LABEL_TYPE@s File" help="restrict to @LABEL_TYPE@s listed in a file" /> | |
297 </xml> | |
298 | |
299 <xml name="macro_restrict" token_type="region" token_label_type="Region" > | |
300 <conditional name="@TYPE@s"> | |
301 <param name="@TYPE@s_src" type="select" label="@LABEL_TYPE@s"> | |
302 <option value="__none__">Do not restrict to @LABEL_TYPE@s</option> | |
303 <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option> | |
304 <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option> | |
277 </param> | 305 </param> |
278 <when value="__none__"/> | 306 <when value="__none__"/> |
279 <when value="regions"> | 307 <when value="@TYPE@s"> |
280 <param name="regions" type="text" value="" optional="true" label="Restrict to comma-separated list of regions" | 308 <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" /> |
281 help="Each region is specifed as: chr or chr:pos or chr:from-to"> | 309 <yield /> |
282 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> | |
283 </param> | |
284 </when> | 310 </when> |
285 <when value="regions_file"> | 311 <when value="@TYPE@s_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" /> | 312 <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" /> |
287 </when> | 313 <yield /> |
314 </when> | |
288 </conditional> | 315 </conditional> |
289 </xml> | 316 </xml> |
317 | |
318 <token name="@PARSE_INTERVALS@"> | |
319 <![CDATA[ | |
320 #set $components = [] | |
321 #for $i in $intervals: | |
322 #set $chrom = str($i.chrom).strip() | |
323 #set $start = str($i.start).strip() | |
324 #set $stop = str($i.stop).strip() | |
325 #if $start or $stop: | |
326 $components.append($chrom + ':' + ($start or '0') + '-' + $stop) | |
327 #else: | |
328 $components.append($chrom) | |
329 #end if | |
330 #end for | |
331 #set $intervals_spec = ','.join($components) | |
332 ]]> | |
333 </token> | |
334 | |
335 <token name="@REGIONS@"> | |
336 <![CDATA[ | |
337 #if $section.regions.regions_src == 'regions': | |
338 #set $intervals = $section.regions.regions | |
339 @PARSE_INTERVALS@ | |
340 --regions '$intervals_spec' | |
341 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: | |
342 #if $regions_path is not None: | |
343 --regions-file '$regions_path' | |
344 #else: | |
345 --regions-file '$section.regions.regions_file' | |
346 #end if | |
347 #end if | |
348 ]]> | |
349 </token> | |
350 | |
351 <token name="@TARGETS@"> | |
352 <![CDATA[ | |
353 #if $targets_path: | |
354 --targets-file "${section.targets.invert_targets_file}${targets_path}" | |
355 #elif $section.targets.targets_src == 'targets': | |
356 #set $intervals = $section.targets.targets | |
357 @PARSE_INTERVALS@ | |
358 --targets '${section.targets.invert_targets_file}$intervals_spec' | |
359 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file: | |
360 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}" | |
361 #end if | |
362 ]]> | |
363 </token> | |
364 | |
290 <token name="@PREPARE_REGIONS_FILE@"> | 365 <token name="@PREPARE_REGIONS_FILE@"> |
291 <![CDATA[ | 366 <![CDATA[ |
292 #set $regions_path = None | 367 #set $regions_path = None |
293 #if 'regions' in $section | 368 #if 'regions' in $section |
294 #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: | 369 #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: |
298 #end if | 373 #end if |
299 #end if | 374 #end if |
300 #end if | 375 #end if |
301 ]]> | 376 ]]> |
302 </token> | 377 </token> |
303 <token name="@REGIONS@"> | 378 |
304 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '': | |
305 --regions '$section.regions.regions' | |
306 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: | |
307 #if $regions_path is not None: | |
308 --regions-file '$regions_path' | |
309 #else: | |
310 --regions-file '$section.regions.regions_file' | |
311 #end if | |
312 #end if | |
313 </token> | |
314 <xml name="macro_targets_file"> | |
315 <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" > | |
316 <yield/> | |
317 </param> | |
318 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" /> | |
319 </xml> | |
320 <token name="@PREPARE_TARGETS_FILE@"> | 379 <token name="@PREPARE_TARGETS_FILE@"> |
321 <![CDATA[ | 380 <![CDATA[ |
322 #set $targets_path = None | 381 #set $targets_path = None |
323 #if 'targets' in $section | 382 #if 'targets' in $section |
324 #if $section.targets.targets_src == 'targets_file': | 383 #if $section.targets.targets_src == 'targets_file': |
331 bgzip -c "$section.targets_file" > $targets_path && | 390 bgzip -c "$section.targets_file" > $targets_path && |
332 tabix -s 1 -b 2 -e 2 $targets_path && | 391 tabix -s 1 -b 2 -e 2 $targets_path && |
333 #end if | 392 #end if |
334 ]]> | 393 ]]> |
335 </token> | 394 </token> |
395 | |
336 <token name="@TARGETS_FILE@"> | 396 <token name="@TARGETS_FILE@"> |
337 <![CDATA[ | 397 <![CDATA[ |
338 #if $targets_path is not None: | 398 #if $targets_path is not None: |
339 --targets-file "${section.invert_targets_file}${targets_path}" | 399 --targets-file "${section.invert_targets_file}${targets_path}" |
340 #elif $section.targets_file: | 400 #elif $section.targets_file: |
341 --targets-file "${section.invert_targets_file}${section.targets_file}" | 401 --targets-file "${section.invert_targets_file}${section.targets_file}" |
342 #end if | |
343 ]]> | |
344 </token> | |
345 | |
346 <xml name="macro_targets"> | |
347 <conditional name="targets"> | |
348 <param name="targets_src" type="select" label="Targets"> | |
349 <option value="__none__">None</option> | |
350 <option value="targets">targets</option> | |
351 <option value="targets_file">targets-file</option> | |
352 </param> | |
353 <when value="__none__"/> | |
354 <when value="targets"> | |
355 <param name="targets" type="text" value="" optional="true" label="Restrict to comma-separated list of targets" | |
356 help="Each target is specifed as: chr or chr:pos or chr:from-to"> | |
357 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> | |
358 </param> | |
359 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" /> | |
360 </when> | |
361 <when value="targets_file"> | |
362 <expand macro="macro_targets_file"> | |
363 </expand> | |
364 </when> | |
365 </conditional> | |
366 </xml> | |
367 <token name="@TARGETS@"> | |
368 <![CDATA[ | |
369 #if $targets_path: | |
370 --targets-file "${section.targets.invert_targets_file}${targets_path}" | |
371 #else: | |
372 #if $section.targets.targets_src == 'targets' and $section.targets.targets != '': | |
373 --targets '${section.targets.invert_targets_file}${section.targets.targets}' | |
374 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file: | |
375 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}" | |
376 #end if | |
377 #end if | 402 #end if |
378 ]]> | 403 ]]> |
379 </token> | 404 </token> |
380 | 405 |
381 <xml name="macro_samples"> | 406 <xml name="macro_samples"> |