Mercurial > repos > iuc > stacks_denovomap

comparison stacks_denovomap.xml @ 8:39d2b6c1c030 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author iuc
date Thu, 27 Apr 2017 04:17:51 -0400
parents 34000c653ae5
children 9f9d39f582f3
comparison
equal deleted inserted replaced
7:2505774ded94 8:39d2b6c1c030
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <command><![CDATA[ 8 <command><![CDATA[
9 #from os.path import splitext 9
10 #import re 10 @CLEAN_EXT@
11 11
12 #if str( $options_usage.rad_analysis_type ) == "genetic": 12 #if str( $options_usage.rad_analysis_type ) == "genetic"
13 #for $input_parent in $options_usage.parent_sequences: 13 #for $input_parent in $options_usage.parent_sequences
14 14 #if $input_parent.is_of_type('fastqsanger')
15 #if $input_parent.is_of_type('fastqsanger'): 15 #set $data_path = $clean_ext($input_parent.element_identifier) + ".fq"
16 #set $data_path = splitext($input_parent.element_identifier)[0] 16 #else if $input_parent.is_of_type('fastqsanger.gz')
17 #set $data_path = re.sub(r'\.1$', '', $data_path) 17 #set $data_path = $clean_ext($input_parent.element_identifier) + ".fq.gz"
18 #set $data_path = $data_path + ".fq" 18 #else
19 #else: 19 #set $data_path = $clean_ext($input_parent.element_identifier) + ".fa"
20 #set $data_path = splitext($input_parent.element_identifier)[0]
21 #set $data_path = re.sub(r'\.1$', '', $data_path)
22 #set $data_path = $data_path + ".fa"
23 #end if 20 #end if
24 21
25 ln -s "${input_parent}" "${data_path}" && 22 ln -s '${input_parent}' '${data_path}' &&
26 #end for 23 #end for
27 24
28 #for $input_progeny in $options_usage.progeny_sequences: 25 #for $input_progeny in $options_usage.progeny_sequences
29 #if $input_progeny: 26 #if $input_progeny
30 #if $input_progeny.is_of_type('fastqsanger'): 27 #if $input_progeny.is_of_type('fastqsanger')
31 #set $data_path = splitext($input_progeny.element_identifier)[0] 28 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".fq"
32 #set $data_path = re.sub(r'\.1$', '', $data_path) 29 #else if $input_progeny.is_of_type('fastqsanger.gz')
33 #set $data_path = $data_path + ".fq" 30 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".fq.gz"
34 #else: 31 #else
35 #set $data_path = splitext($input_progeny.element_identifier)[0] 32 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".fa"
36 #set $data_path = re.sub(r'\.1$', '', $data_path)
37 #set $data_path = $data_path + ".fa"
38 #end if 33 #end if
39 34
40 ln -s "${input_progeny}" "${data_path}" && 35 ln -s '${input_progeny}' '${data_path}' &&
41 #end if 36 #end if
42 #end for 37 #end for
43 #else: 38 #else
44 #for $input_indiv in $options_usage.individual_sample: 39 #for $input_indiv in $options_usage.individual_sample
45 40
46 #if $input_indiv.is_of_type('fastqsanger'): 41 #if $input_indiv.is_of_type('fastqsanger')
47 #set $data_path = splitext($input_indiv.element_identifier)[0] 42 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".fq"
48 #set $data_path = re.sub(r'\.1$', '', $data_path) 43 #else if $input_indiv.is_of_type('fastqsanger.gz')
49 #set $data_path = $data_path + ".fq" 44 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".fq.gz"
50 #else: 45 #else
51 #set $data_path = splitext($input_indiv.element_identifier)[0] 46 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".fa"
52 #set $data_path = re.sub(r'\.1$', '', $data_path)
53 #set $data_path = $data_path + ".fa"
54 #end if 47 #end if
55 48
56 ln -s "${input_indiv}" "${data_path}" && 49 ln -s '${input_indiv}' '${data_path}' &&
57 #end for 50 #end for
58 #end if 51 #end if
59 52
60 mkdir stacks_outputs 53 mkdir stacks_outputs
61 54
63 56
64 denovo_map.pl 57 denovo_map.pl
65 58
66 -T \${GALAXY_SLOTS:-1} 59 -T \${GALAXY_SLOTS:-1}
67 60
68 #if str( $options_usage.rad_analysis_type ) == "genetic": 61 #if str( $options_usage.rad_analysis_type ) == "genetic"
69 #for $input_parent in $options_usage.parent_sequences: 62 #for $input_parent in $options_usage.parent_sequences
70 #if $input_parent.is_of_type('fastqsanger'): 63 #if $input_parent.is_of_type('fastqsanger')
71 #set $data_path = splitext($input_parent.element_identifier)[0] 64 #set $data_path = $clean_ext($input_parent.element_identifier) + ".fq"
72 #set $data_path = re.sub(r'\.1$', '', $data_path) 65 #else if $input_parent.is_of_type('fastqsanger.gz')
73 #set $data_path = $data_path + ".fq" 66 #set $data_path = $clean_ext($input_parent.element_identifier) + ".fq.gz"
74 #else: 67 #else
75 #set $data_path = splitext($input_parent.element_identifier)[0] 68 #set $data_path = $clean_ext($input_parent.element_identifier) + ".fa"
76 #set $data_path = re.sub(r'\.1$', '', $data_path)
77 #set $data_path = $data_path + ".fa"
78 #end if 69 #end if
79 70
80 -p "${data_path}" 71 -p '${data_path}'
81 #end for 72 #end for
82 73
83 -A $options_usage.cross_type 74 -A $options_usage.cross_type
84 75
85 #for $input_progeny in $options_usage.progeny_sequences: 76 #for $input_progeny in $options_usage.progeny_sequences
86 #if $input_progeny: 77 #if $input_progeny
87 #if $input_progeny.is_of_type('fastqsanger'): 78 #if $input_progeny.is_of_type('fastqsanger')
88 #set $data_path = splitext($input_progeny.element_identifier)[0] 79 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".fq"
89 #set $data_path = re.sub(r'\.1$', '', $data_path) 80 #else if $input_progeny.is_of_type('fastqsanger.gz')
90 #set $data_path = $data_path + ".fq" 81 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".fq.gz"
91 #else: 82 #else
92 #set $data_path = splitext($input_progeny.element_identifier)[0] 83 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".fa"
93 #set $data_path = re.sub(r'\.1$', '', $data_path)
94 #set $data_path = $data_path + ".fa"
95 #end if 84 #end if
96 85
97 -r "${data_path}" 86 -r '${data_path}'
98 #end if 87 #end if
99 #end for 88 #end for
100 89
101 #if str($assembly_options.P): 90 #if str($assembly_options.P)
102 -P $assembly_options.P 91 -P $assembly_options.P
103 #end if 92 #end if
104 #else: 93 #else
105 #for $i_indiv, $input_indiv in enumerate($options_usage.individual_sample): 94 #for $i_indiv, $input_indiv in enumerate($options_usage.individual_sample)
106 95
107 #if $input_indiv.is_of_type('fastqsanger'): 96 #if $input_indiv.is_of_type('fastqsanger')
108 #set $data_path = splitext($input_indiv.element_identifier)[0] 97 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".fq"
109 #set $data_path = re.sub(r'\.1$', '', $data_path) 98 #else if $input_indiv.is_of_type('fastqsanger.gz')
110 #set $data_path = $data_path + ".fq" 99 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".fq.gz"
111 #else: 100 #else
112 #set $data_path = splitext($input_indiv.element_identifier)[0] 101 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".fa"
113 #set $data_path = re.sub(r'\.1$', '', $data_path)
114 #set $data_path = $data_path + ".fa"
115 #end if 102 #end if
116 103
117 -s "${data_path}" 104 -s '${data_path}'
118 #end for 105 #end for
119 -O "$options_usage.popmap" 106 -O '$options_usage.popmap'
120 #end if 107 #end if
121 108
122 #if str($assembly_options.m): 109 #if str($assembly_options.m)
123 -m $assembly_options.m 110 -m $assembly_options.m
124 #end if 111 #end if
125 #if str($assembly_options.N): 112 #if str($assembly_options.N)
126 -N $assembly_options.N 113 -N $assembly_options.N
127 #end if 114 #end if
128 -M $assembly_options.M 115 -M $assembly_options.M
129 -n $assembly_options.n 116 -n $assembly_options.n
130 $assembly_options.t 117 $assembly_options.t
135 122
136 ## No SQL recording 123 ## No SQL recording
137 -S 124 -S
138 125
139 ## snp_model 126 ## snp_model
140 #if str( $snp_options.select_model.model_type) == "bounded": 127 #if str( $snp_options.select_model.model_type) == "bounded"
141 --bound_low $snp_options.select_model.bound_low 128 --bound_low $snp_options.select_model.bound_low
142 --bound_high $snp_options.select_model.bound_high 129 --bound_high $snp_options.select_model.bound_high
143 --alpha $snp_options.select_model.alpha 130 --alpha $snp_options.select_model.alpha
144 #else if str( $snp_options.select_model.model_type) == "snp": 131 #else if str( $snp_options.select_model.model_type) == "snp"
145 --alpha $snp_options.select_model.alpha 132 --alpha $snp_options.select_model.alpha
146 #end if 133 #end if
147 134
148 -o stacks_outputs 135 -o stacks_outputs
149 136
150 #if str( $options_usage.rad_analysis_type ) == "genetic": 137 #if str( $options_usage.rad_analysis_type ) == "genetic"
151 @NORM_GENOTYPES_OUTPUT_LIGHT@ 138 @NORM_GENOTYPES_OUTPUT_LIGHT@
139 #end if
140
141 ## If input is in gz format, stacks will output gzipped files (no option to control this)
142 && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi
143
144 &&
145
146 stacks_summary.py --stacks-prog denovo_map.pl --res-dir stacks_outputs --logfile stacks_outputs/denovo_map.log --summary stacks_outputs/summary.html
147 #if str( $options_usage.rad_analysis_type ) == "population"
148 --pop-map '$options_usage.popmap'
152 #end if 149 #end if
153 ]]></command> 150 ]]></command>
154 151
155 <inputs> 152 <inputs>
156 <conditional name="options_usage"> 153 <conditional name="options_usage">
157 <param name="rad_analysis_type" type="select" label="Select your usage"> 154 <param name="rad_analysis_type" type="select" label="Select your usage">
158 <option value="genetic" selected="true">Genetic map</option> 155 <option value="genetic" selected="true">Genetic map</option>
159 <option value="population">Population</option> 156 <option value="population">Population</option>
160 </param> 157 </param>
161 <when value="genetic"> 158 <when value="genetic">
162 <param name="parent_sequences" argument="-p" format="fastqsanger,fasta" type="data" multiple="true" label="Files containing parent sequences" help="Files containing parent sequences from a mapping cross (only R1 reads). Dataset names will be used as sample name (no space allowed)." /> 159 <param name="parent_sequences" argument="-p" format="fastqsanger,fastqsanger.gz,fasta" type="data" multiple="true" label="Files containing parent sequences" help="Files containing parent sequences from a mapping cross (only R1 reads). Dataset names will be used as sample name (no space allowed)." />
163 160
164 <param name="progeny_sequences" argument="-r" format="fastqsanger,fasta" type="data" multiple="true" optional="true" label="Files containing progeny sequences" help="files containing progeny sequences from a mapping cross (only R1 reads). Dataset names will be used as sample name (no space allowed)." /> 161 <param name="progeny_sequences" argument="-r" format="fastqsanger,fastqsanger.gz,fasta" type="data" multiple="true" optional="true" label="Files containing progeny sequences" help="files containing progeny sequences from a mapping cross (only R1 reads). Dataset names will be used as sample name (no space allowed)." />
165 162
166 <param name="cross_type" argument="-A" type="select" label="Cross type"> 163 <param name="cross_type" argument="-A" type="select" label="Cross type">
167 <expand macro="cross_types"/> 164 <expand macro="cross_types"/>
168 </param> 165 </param>
169 </when> 166 </when>
170 <when value="population"> 167 <when value="population">
171 <param name="individual_sample" argument="-s" format="fastqsanger,fasta" type="data" multiple="true" label="Files containing an individual sample from a population" help="files containing an individual sample from a population (only R1 reads). Dataset names will be used as sample name (no space allowed)." /> 168 <param name="individual_sample" argument="-s" format="fastqsanger,fastqsanger.gz,fasta" type="data" multiple="true" label="Files containing an individual sample from a population" help="files containing an individual sample from a population (only R1 reads). Dataset names will be used as sample name (no space allowed)." />
172 <param name="popmap" argument="-O" type="data" format="tabular,txt" label="Specify a population map" /> 169 <param name="popmap" argument="-O" type="data" format="tabular,txt" label="Specify a population map" />
173 </when> 170 </when>
174 </conditional> 171 </conditional>
175 172
176 <!-- stack assembly options --> 173 <!-- stack assembly options -->
191 </section> 188 </section>
192 </inputs> 189 </inputs>
193 <outputs> 190 <outputs>
194 <data format="txt" name="output_log" label="denovo_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/denovo_map.log" /> 191 <data format="txt" name="output_log" label="denovo_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/denovo_map.log" />
195 192
193 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
194
196 <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" /> 195 <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" />
197 <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" /> 196 <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />
198 <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" /> 197 <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />
199 198
200 <expand macro="genotypes_output_light"/> 199 <expand macro="genotypes_output_light"/>
230 <output name="output_log"> 229 <output name="output_log">
231 <assert_contents> 230 <assert_contents>
232 <has_text text="denovo_map.pl completed" /> 231 <has_text text="denovo_map.pl completed" />
233 </assert_contents> 232 </assert_contents>
234 </output> 233 </output>
234 <output name="output_summary">
235 <assert_contents>
236 <has_text text="Stacks Statistics" />
237 </assert_contents>
238 </output>
235 239
236 <!-- catalog --> 240 <!-- catalog -->
237 <output name="catalogtags"> 241 <output name="catalogtags">
238 <assert_contents> 242 <assert_contents>
239 <has_text text="catalog generated on" /> 243 <has_text text="catalog generated on" />
310 <output name="output_log"> 314 <output name="output_log">
311 <assert_contents> 315 <assert_contents>
312 <has_text text="denovo_map.pl completed" /> 316 <has_text text="denovo_map.pl completed" />
313 </assert_contents> 317 </assert_contents>
314 </output> 318 </output>
319 <output name="output_summary">
320 <assert_contents>
321 <has_text text="Stacks Statistics" />
322 </assert_contents>
323 </output>
315 324
316 <!-- catalog --> 325 <!-- catalog -->
317 <output name="catalogtags"> 326 <output name="catalogtags">
318 <assert_contents> 327 <assert_contents>
319 <has_text text="catalog generated on" /> 328 <has_text text="catalog generated on" />
390 <output name="output_log"> 399 <output name="output_log">
391 <assert_contents> 400 <assert_contents>
392 <has_text text="denovo_map.pl completed" /> 401 <has_text text="denovo_map.pl completed" />
393 </assert_contents> 402 </assert_contents>
394 </output> 403 </output>
404 <output name="output_summary">
405 <assert_contents>
406 <has_text text="Stacks Statistics" />
407 </assert_contents>
408 </output>
395 409
396 <!-- catalog --> 410 <!-- catalog -->
397 <output name="catalogtags"> 411 <output name="catalogtags">
398 <assert_contents> 412 <assert_contents>
399 <has_text text="catalog generated on" /> 413 <has_text text="catalog generated on" />
432 </assert_contents> 446 </assert_contents>
433 </output> 447 </output>
434 <output name="out_sumstats"> 448 <output name="out_sumstats">
435 <assert_contents> 449 <assert_contents>
436 <has_text text="Smoothed Pi" /> 450 <has_text text="Smoothed Pi" />
451 </assert_contents>
452 </output>
453
454 <!-- samples -->
455 <output_collection name="tags">
456 <element name="PopA_01.tags">
457 <assert_contents>
458 <has_text text="generated on " />
459 </assert_contents>
460 </element>
461 </output_collection>
462 <output_collection name="snps">
463 <element name="PopA_01.snps">
464 <assert_contents>
465 <has_text text="generated on " />
466 </assert_contents>
467 </element>
468 </output_collection>
469 <output_collection name="alleles">
470 <element name="PopA_01.alleles">
471 <assert_contents>
472 <has_text text="generated on " />
473 </assert_contents>
474 </element>
475 </output_collection>
476 <output_collection name="matches">
477 <element name="PopA_01.matches">
478 <assert_contents>
479 <has_text text="generated on " />
480 </assert_contents>
481 </element>
482 </output_collection>
483 </test>
484 <test>
485 <param name="options_usage|rad_analysis_type" value="genetic"/>
486 <param name="options_usage|parent_sequences" value="demultiplexed/PopA_01.1.fq.gzip" ftype="fastqsanger.gz" />
487 <output name="output_log">
488 <assert_contents>
489 <has_text text="denovo_map.pl completed" />
490 </assert_contents>
491 </output>
492 <output name="output_summary">
493 <assert_contents>
494 <has_text text="Stacks Statistics" />
495 </assert_contents>
496 </output>
497
498 <!-- catalog -->
499 <output name="catalogtags">
500 <assert_contents>
501 <has_text text="catalog generated on" />
502 </assert_contents>
503 </output>
504 <output name="catalogsnps">
505 <assert_contents>
506 <has_text text="catalog generated on" />
507 </assert_contents>
508 </output>
509 <output name="catalogalleles">
510 <assert_contents>
511 <has_text text="catalog generated on" />
512 </assert_contents>
513 </output>
514
515 <!-- genotypes -->
516 <output name="out_generic_haplo">
517 <assert_contents>
518 <has_text text="Catalog ID" />
519 </assert_contents>
520 </output>
521 <output name="out_sql_markers">
522 <assert_contents>
523 <has_text text="Total Genotypes" />
524 </assert_contents>
525 </output>
526 <output name="out_joinmap">
527 <assert_contents>
528 <has_text text="batch_1.genotypes_" />
529 </assert_contents>
530 </output>
531 <output name="out_sql_genotypes">
532 <assert_contents>
533 <has_text text="SQL ID" />
437 </assert_contents> 534 </assert_contents>
438 </output> 535 </output>
439 536
440 <!-- samples --> 537 <!-- samples -->
441 <output_collection name="tags"> 538 <output_collection name="tags">