Mercurial > repos > iuc > stacks2_gstacks

comparison stacks_gstacks.xml @ 1:8b6aa27346b7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author iuc
date Mon, 30 Sep 2019 14:10:49 -0400
parents 6e4b604a1920
children 30efa5dfbaf6
comparison
equal deleted inserted replaced
0:6e4b604a1920 1:8b6aa27346b7
9 <expand macro="version_cmd"/> 9 <expand macro="version_cmd"/>
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 @FASTQ_INPUT_FUNCTIONS@ 11 @FASTQ_INPUT_FUNCTIONS@
12 12
13 mkdir bam_inputs stacks_outputs && 13 mkdir bam_inputs stacks_outputs &&
14
15 ## annoyingly gstacks creates stacks_output/gstacks.log
16 ## instead of just writing to stderr as the other tools
17 ## hence we do not use the tokens and return populations.log as log file and take the stderr
18 #if $output_log
19 ln -s '$output_log' stacks_outputs/gstacks.log &&
20 #end if
21
14 #if $mode_cond.mode_select == "denovo" and not $popmap: 22 #if $mode_cond.mode_select == "denovo" and not $popmap:
15 ## since collections have no len .. yet 23 ## since collections have no len .. yet
16 #try: 24 #try:
17 #set count = len($input_bam) 25 #set count = len($input_bam)
18 #except: 26 #except:
86 #else 94 #else
87 && (samtools view -b bam_inputs/alignments.bam || true) 2> /dev/null > stacks_outputs/alignments.bam 95 && (samtools view -b bam_inputs/alignments.bam || true) 2> /dev/null > stacks_outputs/alignments.bam
88 #end if 96 #end if
89 #end if 97 #end if
90 98
91
92 ## annoyingly gstacks creates stacks_output/gstacks.log
93 ## instead of just writing to stderr as the other tools
94 ## hence we do not use the tokens and return populations.log as log file and take the stderr
95 #if $output_log
96 && mv stacks_outputs/gstacks.log $output_log
97 #end if
98
99 @EXTRACT_VCF@ 99 @EXTRACT_VCF@
100 100
101 ## TODO extract individual distributions from stacks_outputs/gstacks.log.distribs 101 ## TODO extract individual distributions from stacks_outputs/gstacks.log.distribs
102 ## alternative extra tool 102 ## alternative extra tool
103 ## for i in \$(stacks-dist-extract stacks_outputs/gstacks.log.distribs) 103 ## for i in \$(stacks-dist-extract stacks_outputs/gstacks.log.distribs)
248 <param name="gt_alpha" value="0.1" /> 248 <param name="gt_alpha" value="0.1" />
249 </conditional> 249 </conditional>
250 <param name="add_log" value="yes" /> 250 <param name="add_log" value="yes" />
251 <assert_command> 251 <assert_command>
252 <has_text text="--ignore-pe-reads" /> 252 <has_text text="--ignore-pe-reads" />
253 <has_text text="--rm-pcr-duplicates" />
254 <has_text text="--kmer-length 23" /> 253 <has_text text="--kmer-length 23" />
255 <has_text text="--max-debruijn-reads 666" /> 254 <has_text text="--max-debruijn-reads 666" />
256 <has_text text="--min-kmer-cov 3" /> 255 <has_text text="--min-kmer-cov 3" />
257 <has_text text="--write-alignments" /> 256 <has_text text="--write-alignments" />
258 <has_text text="--model marukihigh" /> 257 <has_text text="--model marukihigh" />
268 <param name="input_bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/> 267 <param name="input_bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/>
269 <conditional name="mode_cond"> 268 <conditional name="mode_cond">
270 <param name="mode_select" value="refbased"/> 269 <param name="mode_select" value="refbased"/>
271 <conditional name="paired_cond"> 270 <conditional name="paired_cond">
272 <param name="paired_select" value=""/> 271 <param name="paired_select" value=""/>
273 <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes to much of the test data and gstacks fails--> 272 <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes too much of the test data and gstacks fails-->
274 <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" /> 273 <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" />
275 </conditional> 274 </conditional>
276 </conditional> 275 </conditional>
277 <param name="add_log" value="yes" /> 276 <param name="add_log" value="yes" />
278 <assert_command> 277 <assert_command>
279 <has_text text="-I bam_inputs" /> 278 <not_has_text text="-I bam_inputs" />
280 <not_has_text text="-B " /> 279 <has_text text="-B " />
281 <has_text text="--rm-unpaired-reads" /> 280 <not_has_text text="--rm-unpaired-reads" />
282 <has_text text="--rm-pcr-duplicates" /> 281 <has_text text="--rm-pcr-duplicates" />
283 </assert_command> 282 </assert_command>
284 </test> 283 </test>
285 <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model --> 284 <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model -->
286 <test expect_num_outputs="2"> 285 <test expect_num_outputs="2">
294 <conditional name="advanced_cond"> 293 <conditional name="advanced_cond">
295 <param name="advanced_select" value="yes" /> 294 <param name="advanced_select" value="yes" />
296 <param name="min_mapq" value="23" /> 295 <param name="min_mapq" value="23" />
297 <param name="max_clipped" value="0.23" /> 296 <param name="max_clipped" value="0.23" />
298 <param name="max_insert_len" value="666" /> 297 <param name="max_insert_len" value="666" />
299 <param name="details" value="--detailed"/> 298 <param name="details" value="--details"/>
300 <param name="phasing_cooccurrences_thr_min" value="2"/> 299 <param name="phasing_cooccurrences_thr_min" value="2"/>
301 <param name="phasing_cooccurrences_thr_max" value="3"/> 300 <param name="phasing_cooccurrences_thr_max" value="3"/>
302 <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" /> 301 <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" />
303 </conditional> 302 </conditional>
304 </conditional> 303 </conditional>
305 <param name="model_cond|model" value="snp"/> 304 <param name="model_cond|model" value="snp"/>
306 <param name="model_cond|gt_alpha" value="0.1" /> 305 <param name="model_cond|gt_alpha" value="0.1" />
307 <param name="model_cond|var_alpha" value="0.1" /> 306 <param name="model_cond|var_alpha" value="0.1" />
308 <param name="add_log" value="yes" /> 307 <param name="add_log" value="yes" />
309 <assert_command> 308 <assert_command>
310 <not_has_text text="-I bam_inputs" /> 309 <has_text text="-I bam_inputs" />
311 <has_text text="-B " /> 310 <not_has_text text="-B " />
312 <has_text text="--unpaired" /> 311 <has_text text="--unpaired" />
313 <has_text text="--min-mapq 23" /> 312 <has_text text="--min-mapq 23" />
314 <has_text text="--max-clipped 0.23" /> 313 <has_text text="--max-clipped 0.23" />
315 <has_text text="--max-insert-len 666" /> 314 <has_text text="--max-insert-len 666" />
316 <has_text text="--detailed" /> 315 <has_text text="--details" />
317 <has_text text="--phasing-cooccurrences-thr-range 2,3" /> 316 <has_text text="--phasing-cooccurrences-thr-range 2,3" />
318 <has_text text="--phasing-dont-prune-hets" /> 317 <has_text text="--phasing-dont-prune-hets" />
319 <has_text text="--model snp" /> 318 <has_text text="--model snp" />
320 <has_text text="--gt-alpha 0.1" /> 319 <has_text text="--gt-alpha 0.1" />
321 </assert_command> 320 </assert_command>
331 <param name="paired_select" value="--ignore-pe-reads"/> 330 <param name="paired_select" value="--ignore-pe-reads"/>
332 </conditional> 331 </conditional>
333 </conditional> 332 </conditional>
334 <param name="add_log" value="yes" /> 333 <param name="add_log" value="yes" />
335 <assert_command> 334 <assert_command>
336 <has_text text="-I bam_inputs" /> 335 <not_has_text text="-I bam_inputs" />
337 <not_has_text text="-B " /> 336 <has_text text="-B " />
338 <has_text text="--ignore-pe-reads" /> 337 <has_text text="--ignore-pe-reads" />
339 </assert_command> 338 </assert_command>
340 <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output> 339 <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
341 <output_collection name="gstacks_out" type="list" count="2"/> 340 <output_collection name="gstacks_out" type="list" count="2"/>
342 </test> 341 </test>