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comparison stacks_populations.xml @ 4:d0b325dfe508 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
author iuc
date Mon, 26 Sep 2016 11:44:41 -0400
parents 2ac5c9616748
children f5115df39480
comparison
equal deleted inserted replaced
3:2ac5c9616748 4:d0b325dfe508
1 <tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.1"> 1 <tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.0">
2 <description>analyze a population of individual samples ('populations' program)</description> 2 <description>analyze a population of individual samples ('populations' program)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
10 10
11 mkdir stacks_outputs 11 mkdir stacks_outputs
12 12
13 && 13 &&
14 14
15 #for $input_file in $options_usage.input_col: 15 #if str($options_usage.input_type) == 'stacks':
16 #set $filename = str($input_file.element_identifier) 16 #for $input_file in $options_usage.input_col:
17 #if not $filename.endswith('.tsv'): 17 #set $filename = str($input_file.element_identifier)
18 #set $filename = $filename + ".tsv" 18 #if not $filename.endswith('.tsv'):
19 #end if 19 #set $filename = $filename + ".tsv"
20 #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename): 20 #end if
21 ln -s "${input_file}" "stacks_outputs/${filename}" && 21 #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename):
22 #end if 22 ln -s "${input_file}" "stacks_outputs/${filename}" &&
23 #end for 23 #end if
24 #end for
25 #end if
24 26
25 populations 27 populations
26 28
27 -t \${GALAXY_SLOTS:-1} 29 -t \${GALAXY_SLOTS:-1}
28 30
29 -P stacks_outputs 31 #if str($options_usage.input_type) == 'vcf':
32 -V "$options_usage.input_vcf"
33 #else:
34 -P stacks_outputs
35 -b $advanced_options.batchid
36 #end if
37
30 -M "$options_usage.popmap" 38 -M "$options_usage.popmap"
31 39
32 ## Data filtering 40 ## Data filtering
33 $options_filtering.write_single_snp 41 $options_filtering.write_single_snp
34 $options_filtering.write_random_snp 42 $options_filtering.write_random_snp
109 -B "$advanced_options.blacklist" 117 -B "$advanced_options.blacklist"
110 #end if 118 #end if
111 #if $advanced_options.whitelist: 119 #if $advanced_options.whitelist:
112 -W "$advanced_options.whitelist" 120 -W "$advanced_options.whitelist"
113 #end if 121 #end if
114 -b $advanced_options.batchid
115 ]]></command> 122 ]]></command>
116 123
117 <inputs> 124 <inputs>
118 <section name="options_usage" title="Input" expanded="true"> 125 <conditional name="options_usage">
119 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" /> 126 <param name="input_type" type="select" label="Input type" help="select input file type" >
120 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-M" /> 127 <option value="stacks">Stacks output</option>
121 </section> 128 <!--option value="vcf">VCF file</option--> <!-- broken in 1.42 -->
129 </param>
130 <when value="stacks">
131 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" argument="-P" />
132 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-M" />
133 </when>
134 <when value="vcf">
135 <param name="input_vcf" format="vcf" type="data" label="VCF file" argument="-V" />
136 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-M" />
137 </when>
138 </conditional>
122 139
123 <section name="options_filtering" title="Data filtering options" expanded="true"> 140 <section name="options_filtering" title="Data filtering options" expanded="true">
124 141
125 <param name="minperc" argument="-r" type="float" value="0.5" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population" /> 142 <param name="minperc" argument="-r" type="float" value="0.5" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population" />
126 <param name="minpop" argument="-p" type="integer" value="2" label="Minimum number of populations a locus must be present in to process a locus" /> 143 <param name="minpop" argument="-p" type="integer" value="2" label="Minimum number of populations a locus must be present in to process a locus" />
223 <expand macro="populations_output_full"/> 240 <expand macro="populations_output_full"/>
224 </outputs> 241 </outputs>
225 242
226 <tests> 243 <tests>
227 <test> 244 <test>
245 <param name="options_usage|input_type" value="stacks" />
228 <param name="options_usage|input_col"> 246 <param name="options_usage|input_col">
229 <collection type="list"> 247 <collection type="list">
230 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" /> 248 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
231 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" /> 249 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
232 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" /> 250 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
290 <has_text text="Smoothed Pi" /> 308 <has_text text="Smoothed Pi" />
291 </assert_contents> 309 </assert_contents>
292 </output> 310 </output>
293 <output name="out_vcf"> 311 <output name="out_vcf">
294 <assert_contents> 312 <assert_contents>
295 <has_text text="fileformat=VCFv4.0" /> 313 <has_text text="fileformat=VCFv4.2" />
296 </assert_contents> 314 </assert_contents>
297 </output> 315 </output>
298 <output name="out_treemix_pop"> 316 <output name="out_treemix_pop">
299 <assert_contents> 317 <assert_contents>
300 <has_text text="TreeMix v1.1;" /> 318 <has_text text="TreeMix v1.1;" />
304 <assert_contents> 322 <assert_contents>
305 <has_text text="AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC" /> 323 <has_text text="AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC" />
306 </assert_contents> 324 </assert_contents>
307 </output> 325 </output>
308 </test> 326 </test>
327 <!--test>
328 <param name="options_usage|input_type" value="vcf" />
329 <param name="options_usage|input_vcf" value="populations/batch_1.vcf" />
330 <param name="options_usage|popmap" ftype="tabular" value="denovo_map/popmap.tsv" />
331 <param name="options_filtering|correction_select|correction" value="p_value" />
332
333 <param name="populations_output|ordered_export" value="true" />
334 <param name="populations_output|vcf" value="true" />
335 <param name="populations_output|vcf_haplotypes" value="true" />
336 <param name="populations_output|genepop" value="true" />
337 <param name="populations_output|structure" value="true" />
338 <param name="populations_output|fasta" value="true" />
339 <param name="populations_output|fasta_strict" value="true" />
340 <param name="populations_output|hzar" value="true" />
341 <param name="populations_output|phase" value="true" />
342 <param name="populations_output|fastphase" value="true" />
343 <param name="populations_output|beagle" value="true" />
344 <param name="populations_output|beagle_phased" value="true" />
345 <param name="populations_output|plink" value="true" />
346 <param name="populations_output|phylip" value="true" />
347 <param name="populations_output|phylip_var" value="true" />
348 <param name="populations_output|phylip_var_all" value="true" />
349 <param name="populations_output|treemix" value="true" />
350
351 <param name="populations_output|options_genomic|genomic" value="true" />
352 <param name="populations_output|options_genomic|enzyme" value="ecoRI" /-->
353
354 <!-- populations -->
355 <!--output name="out_haplotypes">
356 <assert_contents>
357 <has_text text="PopA_01" />
358 </assert_contents>
359 </output>
360 <output name="out_hapstats">
361 <assert_contents>
362 <has_text text="Smoothed Gene Diversity" />
363 </assert_contents>
364 </output>
365 <output name="out_populations_log">
366 <assert_contents>
367 <has_text text="populations version" />
368 </assert_contents>
369 </output>
370 <output name="out_sumstats_sum">
371 <assert_contents>
372 <has_text text="Polymorphic Sites" />
373 </assert_contents>
374 </output>
375 <output name="out_sumstats">
376 <assert_contents>
377 <has_text text="Smoothed Pi" />
378 </assert_contents>
379 </output>
380 <output name="out_vcf">
381 <assert_contents>
382 <has_text text="fileformat=VCFv4.2" />
383 </assert_contents>
384 </output>
385 <output name="out_treemix_pop">
386 <assert_contents>
387 <has_text text="TreeMix v1.1;" />
388 </assert_contents>
389 </output>
390 <output name="out_fasta">
391 <assert_contents>
392 <has_text text="AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC" />
393 </assert_contents>
394 </output>
395 </test--> <!-- broken in 1.42 -->
309 </tests> 396 </tests>
310 <help> 397 <help>
311 <![CDATA[ 398 <![CDATA[
312 .. class:: infomark 399 .. class:: infomark
313 400