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comparison bcftools_mpileup.xml @ 23:e1c8ab368943 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 08:00:58 +0000
parents 2f6e26a65721
children
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22:2f6e26a65721 23:e1c8ab368943
1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@"> 1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description> 2 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
3 <macros> 3 <macros>
4 <token name="@EXECUTABLE@">mpileup</token> 4 <token name="@EXECUTABLE@">mpileup</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <xml name="bam_flag_options"> 6 <xml name="bam_flag_options">
15 <option value="256">The alignment or this read is not primary</option> 15 <option value="256">The alignment or this read is not primary</option>
16 <option value="512">The read fails platform/vendor quality checks</option> 16 <option value="512">The read fails platform/vendor quality checks</option>
17 <option value="1024">The read is a PCR or optical duplicate</option> 17 <option value="1024">The read is a PCR or optical duplicate</option>
18 </xml> 18 </xml>
19 </macros> 19 </macros>
20 <expand macro="bio_tools" /> 20 <expand macro="bio_tools"/>
21 <expand macro="requirements"> 21 <expand macro="requirements">
22 <expand macro="samtools_requirement"/> 22 <expand macro="samtools_requirement"/>
23 </expand> 23 </expand>
24 <expand macro="version_command" /> 24 <expand macro="version_command"/>
25 <command detect_errors="aggressive"><![CDATA[ 25 <command detect_errors="aggressive"><![CDATA[
26 #import re 26 #import re
27 #set bam_list = [] 27 #set bam_list = []
28 #if $input.input_number == 'single': 28 #if $input.input_number == 'single':
29 #set $input_base = $re.sub('\W','_',$input.input_bam.display_name.replace('.bam','').replace('.cram','')) 29 #set $input_base = $re.sub('\W','_',$input.input_bam.display_name.replace('.bam','').replace('.cram',''))
180 ${pasted_data} 180 ${pasted_data}
181 ]]> 181 ]]>
182 </configfile> 182 </configfile>
183 </configfiles> 183 </configfiles>
184 <inputs> 184 <inputs>
185
186 <conditional name="input"> 185 <conditional name="input">
187 <param name="input_number" type="select" label="Alignment Inputs"> 186 <param name="input_number" type="select" label="Alignment Inputs">
188 <option value="single">Single BAM/CRAM</option> 187 <option value="single">Single BAM/CRAM</option>
189 <option value="multiple">Multiple BAM/CRAMs</option> 188 <option value="multiple">Multiple BAM/CRAMs</option>
190 </param> 189 </param>
191 <when value="single"> 190 <when value="single">
192 <param name="input_bam" type="data" format="bam,cram" label="Input BAM/CRAM" /> 191 <param name="input_bam" type="data" format="bam,cram" label="Input BAM/CRAM"/>
193 </when> 192 </when>
194 <when value="multiple"> 193 <when value="multiple">
195 <param name="input_bams" type="data" format="bam,cram" multiple="true" label="Input BAM/CRAMs" /> 194 <param name="input_bams" type="data" format="bam,cram" multiple="true" label="Input BAM/CRAMs"/>
196 </when> 195 </when>
197 </conditional> 196 </conditional>
198
199 <conditional name="reference_source"> 197 <conditional name="reference_source">
200 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> 198 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
201 <option value="cached">Locally cached</option> 199 <option value="cached">Locally cached</option>
202 <option value="history">History</option> 200 <option value="history">History</option>
203 <option value="none">No Reference</option> 201 <option value="none">No Reference</option>
206 <param name="ref_file" type="select" label="Select reference genome"> 204 <param name="ref_file" type="select" label="Select reference genome">
207 <options from_data_table="fasta_indexes"/> 205 <options from_data_table="fasta_indexes"/>
208 </param> 206 </param>
209 </when> 207 </when>
210 <when value="history"> 208 <when value="history">
211 <param name="ref_file" type="data" format="fasta" label="Genome Reference" /> 209 <param name="ref_file" type="data" format="fasta" label="Genome Reference"/>
212 </when> 210 </when>
213 <when value="none"/> 211 <when value="none"/>
214 </conditional> 212 </conditional>
215
216 <section name="sec_indel" expanded="false" title="Indel Calling"> 213 <section name="sec_indel" expanded="false" title="Indel Calling">
217 <conditional name="perform_indel_calling"> 214 <conditional name="perform_indel_calling">
218 <param name="perform_indel_calling_selector" type="select" label="Perform INDEL calling"> 215 <param name="perform_indel_calling_selector" type="select" label="Perform INDEL calling">
219 <option selected="True" value="perform_indel_calling_def">Perform INDEL calling using default options</option> 216 <option selected="True" value="perform_indel_calling_def">Perform INDEL calling using default options</option>
220 <option value="perform_indel_calling">Perform INDEL calling and set advanced options</option> 217 <option value="perform_indel_calling">Perform INDEL calling and set advanced options</option>
221 <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option> 218 <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option>
222 </param> 219 </param>
223 <when value="perform_indel_calling_def" /> 220 <when value="perform_indel_calling_def"/>
224 <when value="perform_indel_calling"> 221 <when value="perform_indel_calling">
225 <param name="gap_open_sequencing_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" help="--open-prob; Reducing this value leads to more indel calls; default=40"/> 222 <param name="gap_open_sequencing_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" help="--open-prob; Reducing this value leads to more indel calls; default=40"/>
226 <param name="gap_extension_sequencing_error_probability" type="integer" value="20" label="Phred-scaled gap extension sequencing error probability" help="--ext-prob; Reducing this value leads to longer indels. default=20"/> 223 <param name="gap_extension_sequencing_error_probability" type="integer" value="20" label="Phred-scaled gap extension sequencing error probability" help="--ext-prob; Reducing this value leads to longer indels. default=20"/>
227 <param name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" label="Coefficient for modeling homopolymer errors." help="--tandem-qual; default=100"/> 224 <param name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" label="Coefficient for modeling homopolymer errors." help="--tandem-qual; default=100"/>
228 <param name="skip_indel_calling_above_sample_depth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" help="--max-idepth; default=250"/> 225 <param name="skip_indel_calling_above_sample_depth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" help="--max-idepth; default=250"/>
232 <param name="gapped_read_per_sample" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Apply --min-ireads and --gap-frac values on a per-sample basis" help="--per-sample-mF; by default both options are applied to reads pooled from all samples"/> 229 <param name="gapped_read_per_sample" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Apply --min-ireads and --gap-frac values on a per-sample basis" help="--per-sample-mF; by default both options are applied to reads pooled from all samples"/>
233 <repeat name="platform_list_repeat" title="Platform for INDEL candidates"> 230 <repeat name="platform_list_repeat" title="Platform for INDEL candidates">
234 <param name="platform_entry" type="text" value="" label="Platform to use for INDEL candidates" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/> 231 <param name="platform_entry" type="text" value="" label="Platform to use for INDEL candidates" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/>
235 </repeat> 232 </repeat>
236 </when> 233 </when>
237 <when value="do_not_perform_indel_calling" /> 234 <when value="do_not_perform_indel_calling"/>
238 </conditional> 235 </conditional>
239 <param argument="--ambig-reads" type="select" optional="true" label="Ambiguous indel reads" help="What to do with ambiguous indel reads that do not span an entire short tandem repeat region: discard ambiguous reads from calling and do not increment high-quality AD depth counters (drop), exclude from calling but increment AD counters proportionally (incAD), exclude from calling and increment the first value of the AD counter (incAD0) "> 236 <param argument="--ambig-reads" type="select" optional="true" label="Ambiguous indel reads" help="What to do with ambiguous indel reads that do not span an entire short tandem repeat region: discard ambiguous reads from calling and do not increment high-quality AD depth counters (drop), exclude from calling but increment AD counters proportionally (incAD), exclude from calling and increment the first value of the AD counter (incAD0) ">
240 <option value="drop">Drop</option> 237 <option value="drop">Drop</option>
241 <option value="incAD">IncAD</option> 238 <option value="incAD">IncAD</option>
242 <option value="incAD0">IncAD0</option> 239 <option value="incAD0">IncAD0</option>
243 </param> 240 </param>
244 <param argument="--indel-bias" type="float" min="0" value="" optional="true" label="Indel bias" help="Skews the indel scores up or down, trading recall (low false-negative) vs precision (low false-positive) [1.0]. In Bcftools 1.12 and earlier this parameter didn’t exist, but had an implied value of 1.0. If you are planning to do heavy filtering of variants, selecting the best quality ones only (favouring precision over recall), it is advisable to set this lower (such as 0.75) while higher depth samples or where you favour recall rates over precision may work better with a higher value such as 2.0" /> 241 <param argument="--indel-bias" type="float" min="0" value="" optional="true" label="Indel bias" help="Skews the indel scores up or down, trading recall (low false-negative) vs precision (low false-positive) [1.0]. In Bcftools 1.12 and earlier this parameter didn’t exist, but had an implied value of 1.0. If you are planning to do heavy filtering of variants, selecting the best quality ones only (favouring precision over recall), it is advisable to set this lower (such as 0.75) while higher depth samples or where you favour recall rates over precision may work better with a higher value such as 2.0"/>
245 <param argument="--indel-size" type="integer" min="0" value="" optional="true" label="Indel size" help="Indel window size to use when assessing the quality of candidate indels. Note that although the window size approximately corresponds to the maximum indel size considered, it is not an exact threshold. Default: 110" /> 242 <param argument="--indel-size" type="integer" min="0" value="" optional="true" label="Indel size" help="Indel window size to use when assessing the quality of candidate indels. Note that although the window size approximately corresponds to the maximum indel size considered, it is not an exact threshold. Default: 110"/>
246 </section> 243 </section>
247
248 <section name="sec_filtering" expanded="false" title="Input Filtering Options"> 244 <section name="sec_filtering" expanded="false" title="Input Filtering Options">
249 <param name="max_reads_per_bam" type="integer" value="250" min="1" label="Max reads per BAM" help="--max-depth; default=250"/> 245 <param name="max_reads_per_bam" type="integer" value="250" min="1" label="Max reads per BAM" help="--max-depth; default=250"/>
250 <param name="ignore_overlaps" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Disable read-pair overlap detection" help="--ignore-overlaps"/> 246 <param name="ignore_overlaps" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Disable read-pair overlap detection" help="--ignore-overlaps"/>
251 <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" help="--count-orphans"/> 247 <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" help="--count-orphans"/>
252 <conditional name="filter_by_flags"> 248 <conditional name="filter_by_flags">
254 <option selected="True" value="nofilter">Do not filter</option> 250 <option selected="True" value="nofilter">Do not filter</option>
255 <option value="filter">Filter by flags to exclude or require</option> 251 <option value="filter">Filter by flags to exclude or require</option>
256 </param> 252 </param>
257 <when value="filter"> 253 <when value="filter">
258 <param argument="--skip-all-set" type="select" display="checkboxes" label="Skip reads with all of the FLAG bits set" multiple="True" help="--skip-all-set"> 254 <param argument="--skip-all-set" type="select" display="checkboxes" label="Skip reads with all of the FLAG bits set" multiple="True" help="--skip-all-set">
259 <expand macro="bam_flag_options" /> 255 <expand macro="bam_flag_options"/>
260 </param> 256 </param>
261 <param argument="--skip-any-set" type="select" display="checkboxes" label="Skip reads with any of the FLAG bits set" multiple="True" help="--skip-any-set"> 257 <param argument="--skip-any-set" type="select" display="checkboxes" label="Skip reads with any of the FLAG bits set" multiple="True" help="--skip-any-set">
262 <expand macro="bam_flag_options" /> 258 <expand macro="bam_flag_options"/>
263 </param> 259 </param>
264 <param argument="--skip-all-unset" type="select" display="checkboxes" label="Skip reads with all of the FLAG bits unset" multiple="True" help="--skip-all-unset"> 260 <param argument="--skip-all-unset" type="select" display="checkboxes" label="Skip reads with all of the FLAG bits unset" multiple="True" help="--skip-all-unset">
265 <expand macro="bam_flag_options" /> 261 <expand macro="bam_flag_options"/>
266 </param> 262 </param>
267 <param argument="--skip-any-unset" type="select" display="checkboxes" label="Skip reads with any of the FLAG bits unset" multiple="True" help="--skip-any-unset"> 263 <param argument="--skip-any-unset" type="select" display="checkboxes" label="Skip reads with any of the FLAG bits unset" multiple="True" help="--skip-any-unset">
268 <expand macro="bam_flag_options" /> 264 <expand macro="bam_flag_options"/>
269 </param> 265 </param>
270 </when> 266 </when>
271 <when value="nofilter" /> 267 <when value="nofilter"/>
272 </conditional> 268 </conditional>
273 <conditional name="quality"> 269 <conditional name="quality">
274 <param label="Quality Options" name="quality_settings" type="select"> 270 <param label="Quality Options" name="quality_settings" type="select">
275 <option value="none" selected="True">defaults</option> 271 <option value="none" selected="True">defaults</option>
276 <option value="adjust">Set base and mapping quality options</option> 272 <option value="adjust">Set base and mapping quality options</option>
289 <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/> 285 <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/>
290 <param name="minimum_base_quality" type="integer" value="13" label="Minimum base quality for a base to be considered" help="--min-BQ; default=13"/> 286 <param name="minimum_base_quality" type="integer" value="13" label="Minimum base quality for a base to be considered" help="--min-BQ; default=13"/>
291 </when> 287 </when>
292 <when value="none"/> 288 <when value="none"/>
293 </conditional> 289 </conditional>
294
295 <conditional name="read_groups"> 290 <conditional name="read_groups">
296 <param name="read_groups_selector" type="select" label="Select read groups to include or exclude" help="--read-groups"> 291 <param name="read_groups_selector" type="select" label="Select read groups to include or exclude" help="--read-groups">
297 <option value="no_limit" selected="True">use defaults</option> 292 <option value="no_limit" selected="True">use defaults</option>
298 <option value="history">From an uploaded text file</option> 293 <option value="history">From an uploaded text file</option>
299 <option value="paste">Paste a list of read groups</option> 294 <option value="paste">Paste a list of read groups</option>
300 <option value="ignore_rg">Ignore RG tags. Treat all reads in one alignment file as one sample. </option> 295 <option value="ignore_rg">Ignore RG tags. Treat all reads in one alignment file as one sample. </option>
301 </param> 296 </param>
302 <when value="history"> 297 <when value="history">
303 <param name="read_groups" format="txt" label="Text file" type="data"> 298 <param name="read_groups" format="txt" label="Text file" type="data">
304 <validator type="dataset_ok_validator" /> 299 <validator type="dataset_ok_validator"/>
305 </param> 300 </param>
306 <param name="rg_action" type="select" label="Include or Exclude these Read Groups"> 301 <param name="rg_action" type="select" label="Include or Exclude these Read Groups">
307 <option value="" selected="true">Include</option> 302 <option value="" selected="true">Include</option>
308 <option value="^">Exclude</option> 303 <option value="^">Exclude</option>
309 </param> 304 </param>
310 </when> 305 </when>
311 <when value="paste"> 306 <when value="paste">
312 <param name="group_paste" type="text" size="10x35" area="true" label="Read groups" help="Paste a list of read groups" /> 307 <param name="group_paste" type="text" size="10x35" area="true" label="Read groups" help="Paste a list of read groups"/>
313 <param name="rg_action" type="select" label="Include or Exclude these Read Groups"> 308 <param name="rg_action" type="select" label="Include or Exclude these Read Groups">
314 <option value="" selected="true">Include</option> 309 <option value="" selected="true">Include</option>
315 <option value="^">Exclude</option> 310 <option value="^">Exclude</option>
316 </param> 311 </param>
317 </when> 312 </when>
318 <when value="ignore_rg" /> 313 <when value="ignore_rg"/>
319 <when value="no_limit" /> 314 <when value="no_limit"/>
320 </conditional> 315 </conditional>
321 </section> 316 </section>
322
323 <section name="sec_restrict" expanded="false" title="Restrict to"> 317 <section name="sec_restrict" expanded="false" title="Restrict to">
324 <expand macro="macro_restrict" /> 318 <expand macro="macro_region_restrict_simple"/>
325 <expand macro="macro_restrict" type="target" label_type="Target"> 319 <expand macro="macro_target_restrict_simple"/>
326 <expand macro="macro_invert_targets" />
327 </expand>
328 </section> 320 </section>
329 <section name="sec_subset" expanded="false" title="Subset Options"> 321 <section name="sec_subset" expanded="false" title="Subset Options">
330 <expand macro="macro_samples" /> 322 <expand macro="macro_samples"/>
331 </section> 323 </section>
332
333 <section name="sec_output_options" expanded="false" title="Output options"> 324 <section name="sec_output_options" expanded="false" title="Output options">
334 <expand macro="macro_output_tags"> 325 <expand macro="macro_output_tags">
335 <option value="DP">DP (Number of high-quality bases)</option> 326 <option value="DP">DP (Number of high-quality bases)</option>
336 <option value="AD">AD (Allelic depth)</option> 327 <option value="AD">AD (Allelic depth)</option>
337 <option value="ADF">ADF (Allelic depth on the forward strand)</option> 328 <option value="ADF">ADF (Allelic depth on the forward strand)</option>
351 output gVCF blocks of homozygous REF calls, with depth (DP) ranges specified by the list of integers. For example, passing 5,15 will group sites into two types of gVCF blocks, the first with minimum per-sample DP from the interval [5,15) and the latter with minimum depth 15 or more. In this example, sites with minimum per-sample depth less than 5 will be printed as separate records, outside of gVCF blocks. 342 output gVCF blocks of homozygous REF calls, with depth (DP) ranges specified by the list of integers. For example, passing 5,15 will group sites into two types of gVCF blocks, the first with minimum per-sample DP from the interval [5,15) and the latter with minimum depth 15 or more. In this example, sites with minimum per-sample depth less than 5 will be printed as separate records, outside of gVCF blocks.
352 </help> 343 </help>
353 <validator type="regex" message="integers separated by commas">^(\d+(,\d+)*)?$</validator> 344 <validator type="regex" message="integers separated by commas">^(\d+(,\d+)*)?$</validator>
354 </param> 345 </param>
355 </section> 346 </section>
356 347 <expand macro="macro_select_output_type"/>
357 <expand macro="macro_select_output_type" />
358
359 </inputs> 348 </inputs>
360 <outputs> 349 <outputs>
361 <expand macro="macro_vcf_output" /> 350 <expand macro="macro_vcf_output"/>
362 </outputs> 351 </outputs>
363 <tests> 352 <tests>
364 <test> 353 <test>
365 <param name="input_number" value="single" /> 354 <conditional name="input">
366 <param name="input_bam" ftype="bam" value="mpileup.1.bam" /> 355 <param name="input_number" value="single"/>
367 <param name="reference_source_selector" value="history" /> 356 <param name="input_bam" ftype="bam" value="mpileup.1.bam"/>
368 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> 357 </conditional>
369 <param name="output_type" value="v" /> 358 <conditional name="reference_source">
370 <output name="output_file"> 359 <param name="reference_source_selector" value="history"/>
371 <assert_contents> 360 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa"/>
372 <has_text text="mpileup" /> 361 </conditional>
373 <has_text text="HG00100" /> 362 <param name="output_type" value="v"/>
374 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;" /> 363 <output name="output_file">
375 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;" /> 364 <assert_contents>
376 </assert_contents> 365 <has_text text="mpileup"/>
377 </output> 366 <has_text text="HG00100"/>
378 </test> 367 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;"/>
379 <test> 368 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;"/>
380 <param name="input_number" value="single" /> 369 </assert_contents>
381 <param name="input_bam" ftype="bam" value="mpileup.1.bam" /> 370 </output>
382 <param name="reference_source_selector" value="cached" /> 371 </test>
383 <param name="ref_file" value="mpileup" /> 372 <test>
384 <param name="quality_settings" value="adjust" /> 373 <conditional name="input">
385 <param name="output_type" value="v" /> 374 <param name="input_number" value="single"/>
386 <output name="output_file"> 375 <param name="input_bam" ftype="bam" value="mpileup.1.bam"/>
387 <assert_contents> 376 </conditional>
388 <has_text text="mpileup" /> 377 <conditional name="reference_source">
389 <has_text text="HG00100" /> 378 <param name="reference_source_selector" value="cached"/>
390 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;" /> 379 <param name="ref_file" value="mpileup"/>
391 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;" /> 380 </conditional>
392 </assert_contents> 381 <section name="sec_filtering">
393 </output> 382 <conditional name="quality">
394 </test> 383 <param name="quality_settings" value="adjust"/>
395 <test> 384 </conditional>
396 <param name="input_number" value="single" /> 385 </section>
397 <param name="input_bam" ftype="cram" value="mpileup.3.cram" /> 386 <param name="output_type" value="v"/>
398 <param name="reference_source_selector" value="history" /> 387 <output name="output_file">
399 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> 388 <assert_contents>
400 <param name="output_type" value="v" /> 389 <has_text text="mpileup"/>
401 <output name="output_file"> 390 <has_text text="HG00100"/>
402 <assert_contents> 391 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;"/>
403 <has_text text="mpileup" /> 392 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;"/>
404 <has_text text="HG00102" /> 393 </assert_contents>
405 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=5;" /> 394 </output>
406 </assert_contents> 395 </test>
407 </output> 396 <test>
408 </test> 397 <conditional name="input">
409 <test> 398 <param name="input_number" value="single"/>
410 <param name="input_number" value="multiple" /> 399 <param name="input_bam" ftype="cram" value="mpileup.3.cram"/>
411 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" /> 400 </conditional>
412 <param name="reference_source_selector" value="history" /> 401 <conditional name="reference_source">
413 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> 402 <param name="reference_source_selector" value="history"/>
403 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa"/>
404 </conditional>
405 <param name="output_type" value="v"/>
406 <output name="output_file">
407 <assert_contents>
408 <has_text text="mpileup"/>
409 <has_text text="HG00102"/>
410 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=5;"/>
411 </assert_contents>
412 </output>
413 </test>
414 <test>
415 <conditional name="input">
416 <param name="input_number" value="multiple"/>
417 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam"/>
418 </conditional>
419 <conditional name="reference_source">
420 <param name="reference_source_selector" value="history"/>
421 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa"/>
422 </conditional>
414 <section name="sec_restrict"> 423 <section name="sec_restrict">
415 <conditional name="regions"> 424 <conditional name="regions">
416 <param name="regions_src" value="regions" /> 425 <param name="regions_src" value="regions"/>
417 <repeat name="regions"> 426 <repeat name="region_specs">
418 <param name="chrom" value="17" /> 427 <param name="chrom" value="17"/>
419 <param name="start" value="100" /> 428 <param name="start" value="100"/>
420 <param name="stop" value="110" /> 429 <param name="stop" value="110"/>
421 </repeat> 430 </repeat>
422 </conditional> 431 </conditional>
423 </section> 432 </section>
424 <param name="output_tags" value="DP,INFO/AD,DV" /> 433 <section name="sec_output_options">
425 <param name="output_type" value="v" /> 434 <param name="output_tags" value="DP,INFO/AD,DV"/>
426 <output name="output_file"> 435 </section>
427 <assert_contents> 436 <param name="output_type" value="v"/>
428 <has_text text="mpileup" /> 437 <output name="output_file">
429 <has_text text="HG00100" /> 438 <assert_contents>
430 <has_text text="HG00101" /> 439 <has_text text="mpileup"/>
431 <has_text text="HG00102" /> 440 <has_text text="HG00100"/>
432 <has_text text="ID=DP," /> 441 <has_text text="HG00101"/>
433 <not_has_text text="17\t111" /> 442 <has_text text="HG00102"/>
434 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=18;AD=17,0;" /> 443 <has_text text="ID=DP,"/>
435 </assert_contents> 444 <not_has_text text="17\t111"/>
436 </output> 445 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=18;AD=17,0;"/>
437 </test> 446 </assert_contents>
438 <test> 447 </output>
439 <param name="input_number" value="multiple" /> 448 </test>
440 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" /> 449 <test>
441 <param name="reference_source_selector" value="history" /> 450 <conditional name="input">
442 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> 451 <param name="input_number" value="multiple"/>
452 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam"/>
453 </conditional>
454 <conditional name="reference_source">
455 <param name="reference_source_selector" value="history"/>
456 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa"/>
457 </conditional>
443 <section name="sec_restrict"> 458 <section name="sec_restrict">
444 <conditional name="targets"> 459 <conditional name="targets">
445 <param name="targets_src" value="targets" /> 460 <param name="targets_src" value="targets"/>
446 <repeat name="targets"> 461 <repeat name="target_specs">
447 <param name="chrom" value="17" /> 462 <param name="chrom" value="17"/>
448 <param name="start" value="100" /> 463 <param name="start" value="100"/>
449 <param name="stop" value="104" /> 464 <param name="stop" value="104"/>
450 </repeat> 465 </repeat>
451 </conditional> 466 </conditional>
452 </section> 467 </section>
453 <param name="output_tags" value="DP,INFO/AD,DV" /> 468 <section name="sec_output_options">
454 <param name="output_type" value="v" /> 469 <param name="output_tags" value="DP,INFO/AD,DV"/>
455 <output name="output_file"> 470 </section>
456 <assert_contents> 471 <param name="output_type" value="v"/>
457 <has_text text="mpileup" /> 472 <output name="output_file">
458 <has_text text="HG00100" /> 473 <assert_contents>
459 <has_text text="HG00101" /> 474 <has_text text="mpileup"/>
460 <has_text text="HG00102" /> 475 <has_text text="HG00100"/>
461 <has_text text="ID=DP," /> 476 <has_text text="HG00101"/>
462 <not_has_text text="17\t105" /> 477 <has_text text="HG00102"/>
463 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=18;AD=17,0;" /> 478 <has_text text="ID=DP,"/>
464 </assert_contents> 479 <not_has_text text="17\t105"/>
465 </output> 480 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=18;AD=17,0;"/>
466 </test> 481 </assert_contents>
467 <test> 482 </output>
468 <param name="input_number" value="multiple" /> 483 </test>
469 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" /> 484 <test>
470 <param name="reference_source_selector" value="history" /> 485 <conditional name="input">
471 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> 486 <param name="input_number" value="multiple"/>
487 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam"/>
488 </conditional>
489 <conditional name="reference_source">
490 <param name="reference_source_selector" value="history"/>
491 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa"/>
492 </conditional>
472 <section name="sec_restrict"> 493 <section name="sec_restrict">
473 <conditional name="regions"> 494 <conditional name="regions">
474 <param name="regions_src" value="regions" /> 495 <param name="regions_src" value="regions"/>
475 <repeat name="regions"> 496 <repeat name="region_specs">
476 <param name="chrom" value="17" /> 497 <param name="chrom" value="17"/>
477 <param name="start" value="1050" /> 498 <param name="start" value="1050"/>
478 <param name="stop" value="1060" /> 499 <param name="stop" value="1060"/>
479 </repeat> 500 </repeat>
480 </conditional> 501 </conditional>
481 </section> 502 </section>
482 <param name="filter_flags" value="filter" /> 503 <section name="sec_filtering">
483 <param name="skip_all_set" value="4,16" /> 504 <conditional name="filter_by_flags">
484 <param name="output_type" value="v" /> 505 <param name="filter_flags" value="filter"/>
485 <output name="output_file"> 506 <param name="skip_all_set" value="4,16"/>
486 <assert_contents> 507 </conditional>
487 <has_text text="mpileup" /> 508 </section>
488 <has_text text="HG00100" /> 509 <param name="output_type" value="v"/>
489 <has_text_matching expression="17\t1050\t.\tA\t" /> 510 <output name="output_file">
511 <assert_contents>
512 <has_text text="mpileup"/>
513 <has_text text="HG00100"/>
514 <has_text_matching expression="17\t1050\t.\tA\t"/>
490 </assert_contents> 515 </assert_contents>
491 </output> 516 </output>
492 <assert_command> 517 <assert_command>
493 <has_text text="--skip-all-set" /> 518 <has_text text="--skip-all-set"/>
494 </assert_command> 519 </assert_command>
495 </test> 520 </test>
496 <!-- Test indel options--> 521 <!-- Test indel options-->
497 <test> 522 <test>
498 <param name="input_number" value="single" /> 523 <conditional name="input">
499 <param name="input_bam" ftype="bam" value="mpileup.1.bam" /> 524 <param name="input_number" value="single"/>
500 <param name="reference_source_selector" value="history" /> 525 <param name="input_bam" ftype="bam" value="mpileup.1.bam"/>
501 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> 526 </conditional>
527 <conditional name="reference_source">
528 <param name="reference_source_selector" value="history"/>
529 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa"/>
530 </conditional>
502 <section name="sec_indel"> 531 <section name="sec_indel">
503 <param name="ambig_reads" value="drop"/> 532 <param name="ambig_reads" value="drop"/>
504 <param name="indel_bias" value="1"/> 533 <param name="indel_bias" value="1"/>
505 <param name="indel_size" value="110"/> 534 <param name="indel_size" value="110"/>
506 </section> 535 </section>
507 <param name="output_type" value="v" /> 536 <param name="output_type" value="v"/>
508 <output name="output_file"> 537 <output name="output_file">
509 <assert_contents> 538 <assert_contents>
510 <has_text text="mpileup" /> 539 <has_text text="mpileup"/>
511 <has_text text="HG00100" /> 540 <has_text text="HG00100"/>
512 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;" /> 541 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;"/>
513 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;" /> 542 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;"/>
514 </assert_contents> 543 </assert_contents>
515 </output> 544 </output>
516 <assert_command> 545 <assert_command>
517 <has_text text="--ambig-reads" /> 546 <has_text text="--ambig-reads"/>
518 <has_text text="--indel-bias" /> 547 <has_text text="--indel-bias"/>
519 <has_text text="--indel-size" /> 548 <has_text text="--indel-size"/>
520 </assert_command> 549 </assert_command>
521
522 </test> 550 </test>
523 </tests> 551 </tests>
524 <help><![CDATA[ 552 <help><![CDATA[
525 ===================================== 553 =====================================
526 bcftools @EXECUTABLE@ 554 bcftools @EXECUTABLE@
542 @REGIONS_HELP@ 570 @REGIONS_HELP@
543 @TARGETS_HELP@ 571 @TARGETS_HELP@
544 572
545 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 573 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
546 574
547 @BCFTOOLS_WIKI@ 575 @BCFTOOLS_HOWTOS@
548 ]]></help> 576 ]]></help>
549 <expand macro="citations" /> 577 <expand macro="citations"/>
550 </tool> 578 </tool>