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comparison stacks_refmap.xml @ 8:c209e3f3359b 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 04:17:01 -0400
parents 12aa3ad29980
children 1ba1185929c1
comparison
equal deleted inserted replaced
7:14396ffcb253 8:c209e3f3359b
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_alignments: 13 #for $input_parent in $options_usage.parent_alignments
14 #if $input_parent.is_of_type('sam'): 14 #if $input_parent.is_of_type('sam')
15 #set $data_path = splitext($input_parent.element_identifier)[0] 15 #set $data_path = $clean_ext($input_parent.element_identifier) + ".sam"
16 #set $data_path = re.sub(r'\.1$', '', $data_path) 16 #else
17 #set $data_path = $data_path + ".sam" 17 #set $data_path = $clean_ext($input_parent.element_identifier) + ".bam"
18 #else:
19 #set $data_path = splitext($input_parent.element_identifier)[0]
20 #set $data_path = re.sub(r'\.1$', '', $data_path)
21 #set $data_path = $data_path + ".bam"
22 #end if 18 #end if
23 19
24 ln -s "${input_parent}" "${data_path}" && 20 ln -s '${input_parent}' '${data_path}' &&
25 #end for 21 #end for
26 22
27 #for $input_progeny in $options_usage.progeny_alignments: 23 #for $input_progeny in $options_usage.progeny_alignments
28 24
29 #if $input_progeny: 25 #if $input_progeny
30 #if $input_progeny.is_of_type('sam'): 26 #if $input_progeny.is_of_type('sam')
31 #set $data_path = splitext($input_progeny.element_identifier)[0] 27 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".sam"
32 #set $data_path = re.sub(r'\.1$', '', $data_path) 28 #else
33 #set $data_path = $data_path + ".sam" 29 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".bam"
34 #else:
35 #set $data_path = splitext($input_progeny.element_identifier)[0]
36 #set $data_path = re.sub(r'\.1$', '', $data_path)
37 #set $data_path = $data_path + ".bam"
38 #end if 30 #end if
39 31
40 ln -s "${input_progeny}" "${data_path}" && 32 ln -s '${input_progeny}' '${data_path}' &&
41 #end if 33 #end if
42 #end for 34 #end for
43 #else: 35 #else
44 #for $input_indiv in $options_usage.individual_sample: 36 #for $input_indiv in $options_usage.individual_sample
45 37
46 #if $input_indiv.is_of_type('sam'): 38 #if $input_indiv.is_of_type('sam')
47 #set $data_path = splitext($input_indiv.element_identifier)[0] 39 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".sam"
48 #set $data_path = re.sub(r'\.1$', '', $data_path) 40 #else
49 #set $data_path = $data_path + ".sam" 41 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".bam"
50 #else:
51 #set $data_path = splitext($input_indiv.element_identifier)[0]
52 #set $data_path = re.sub(r'\.1$', '', $data_path)
53 #set $data_path = $data_path + ".bam"
54 #end if 42 #end if
55 43
56 ln -s "${input_indiv}" "${data_path}" && 44 ln -s '${input_indiv}' '${data_path}' &&
57 #end for 45 #end for
58 #end if 46 #end if
59 47
60 mkdir stacks_outputs 48 mkdir stacks_outputs
61 49
63 51
64 ref_map.pl 52 ref_map.pl
65 53
66 -T \${GALAXY_SLOTS:-1} 54 -T \${GALAXY_SLOTS:-1}
67 55
68 #if str( $options_usage.rad_analysis_type ) == "genetic": 56 #if str( $options_usage.rad_analysis_type ) == "genetic"
69 #for $input_parent in $options_usage.parent_alignments: 57 #for $input_parent in $options_usage.parent_alignments
70 #if $input_parent.is_of_type('sam'): 58 #if $input_parent.is_of_type('sam')
71 #set $data_path = splitext($input_parent.element_identifier)[0] 59 #set $data_path = $clean_ext($input_parent.element_identifier) + ".sam"
72 #set $data_path = re.sub(r'\.1$', '', $data_path) 60 #else
73 #set $data_path = $data_path + ".sam" 61 #set $data_path = $clean_ext($input_parent.element_identifier) + ".bam"
74 #else:
75 #set $data_path = splitext($input_parent.element_identifier)[0]
76 #set $data_path = re.sub(r'\.1$', '', $data_path)
77 #set $data_path = $data_path + ".bam"
78 #end if 62 #end if
79 63
80 -p "${data_path}" 64 -p '${data_path}'
81 #end for 65 #end for
82 66
83 -A $options_usage.cross_type 67 -A $options_usage.cross_type
84 68
85 #for $input_progeny in $options_usage.progeny_alignments: 69 #for $input_progeny in $options_usage.progeny_alignments
86 #if $input_progeny: 70 #if $input_progeny
87 #if $input_progeny.is_of_type('sam'): 71 #if $input_progeny.is_of_type('sam')
88 #set $data_path = splitext($input_progeny.element_identifier)[0] 72 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".sam"
89 #set $data_path = re.sub(r'\.1$', '', $data_path) 73 #else
90 #set $data_path = $data_path + ".sam" 74 #set $data_path = $clean_ext($input_progeny.element_identifier) + ".bam"
91 #else:
92 #set $data_path = splitext($input_progeny.element_identifier)[0]
93 #set $data_path = re.sub(r'\.1$', '', $data_path)
94 #set $data_path = $data_path + ".bam"
95 #end if 75 #end if
96 76
97 -r "${data_path}" 77 -r '${data_path}'
98 #end if 78 #end if
99 #end for 79 #end for
100 #else: 80 #else
101 #for $input_indiv in $options_usage.individual_sample: 81 #for $input_indiv in $options_usage.individual_sample
102 82
103 #if $input_indiv.is_of_type('sam'): 83 #if $input_indiv.is_of_type('sam')
104 #set $data_path = splitext($input_indiv.element_identifier)[0] 84 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".sam"
105 #set $data_path = re.sub(r'\.1$', '', $data_path) 85 #else
106 #set $data_path = $data_path + ".sam" 86 #set $data_path = $clean_ext($input_indiv.element_identifier) + ".bam"
107 #else:
108 #set $data_path = splitext($input_indiv.element_identifier)[0]
109 #set $data_path = re.sub(r'\.1$', '', $data_path)
110 #set $data_path = $data_path + ".bam"
111 #end if 87 #end if
112 88
113 -s "${data_path}" 89 -s '${data_path}'
114 #end for 90 #end for
115 -O "$options_usage.popmap" 91 -O '$options_usage.popmap'
116 #end if 92 #end if
117 93
118 #if str($m): 94 #if str($m)
119 -m $m 95 -m $m
120 #end if 96 #end if
121 #if str($P): 97 #if str($P)
122 -P $P 98 -P $P
123 #end if 99 #end if
124 100
125 ## Batch description 101 ## Batch description
126 -b 1 102 -b 1
127 103
128 ## No SQL recording 104 ## No SQL recording
129 -S 105 -S
130 106
131 ## snp_model 107 ## snp_model
132 #if str( $snp_options.select_model.model_type) == "bounded": 108 #if str( $snp_options.select_model.model_type) == "bounded"
133 --bound_low $snp_options.select_model.bound_low 109 --bound_low $snp_options.select_model.bound_low
134 --bound_high $snp_options.select_model.bound_high 110 --bound_high $snp_options.select_model.bound_high
135 --alpha $snp_options.select_model.alpha 111 --alpha $snp_options.select_model.alpha
136 #else if str( $snp_options.select_model.model_type) == "snp": 112 #else if str( $snp_options.select_model.model_type) == "snp"
137 --alpha $snp_options.select_model.alpha 113 --alpha $snp_options.select_model.alpha
138 #end if 114 #end if
139 115
140 -o stacks_outputs 116 -o stacks_outputs
141 117
142 #if str( $options_usage.rad_analysis_type ) == "genetic": 118 #if str( $options_usage.rad_analysis_type ) == "genetic"
143 @NORM_GENOTYPES_OUTPUT_LIGHT@ 119 @NORM_GENOTYPES_OUTPUT_LIGHT@
144 #end if 120 #end if
145 121
146 ## If input is in bam format, stacks will output gzipped files (no option to control this) 122 ## If input is in bam format, stacks will output gzipped files (no option to control this)
147 && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi 123 && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi
124
125 &&
126
127 stacks_summary.py --stacks-prog ref_map.pl --res-dir stacks_outputs --logfile stacks_outputs/ref_map.log --summary stacks_outputs/summary.html
128 #if str( $options_usage.rad_analysis_type ) == "population":
129 --pop-map '$options_usage.popmap'
130 #end if
148 ]]></command> 131 ]]></command>
149 132
150 <inputs> 133 <inputs>
151 <conditional name="options_usage"> 134 <conditional name="options_usage">
152 <param name="rad_analysis_type" type="select" label="Select your usage"> 135 <param name="rad_analysis_type" type="select" label="Select your usage">
176 </section> 159 </section>
177 </inputs> 160 </inputs>
178 <outputs> 161 <outputs>
179 <data format="txt" name="output_log" label="ref_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/ref_map.log" /> 162 <data format="txt" name="output_log" label="ref_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/ref_map.log" />
180 163
164 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
165
181 <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" /> 166 <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" />
182 <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" /> 167 <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" />
183 <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" /> 168 <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" />
184 169
185 <expand macro="genotypes_output_light"/> 170 <expand macro="genotypes_output_light"/>
215 <output name="output_log"> 200 <output name="output_log">
216 <assert_contents> 201 <assert_contents>
217 <has_text text="ref_map.pl completed" /> 202 <has_text text="ref_map.pl completed" />
218 </assert_contents> 203 </assert_contents>
219 </output> 204 </output>
205 <output name="output_summary">
206 <assert_contents>
207 <has_text text="Stacks Statistics" />
208 </assert_contents>
209 </output>
220 210
221 <!-- catalog --> 211 <!-- catalog -->
222 <output name="catalogsnps"> 212 <output name="catalogsnps">
223 <assert_contents> 213 <assert_contents>
224 <has_text text="catalog generated" /> 214 <has_text text="catalog generated" />
304 <output name="output_log"> 294 <output name="output_log">
305 <assert_contents> 295 <assert_contents>
306 <has_text text="ref_map.pl completed" /> 296 <has_text text="ref_map.pl completed" />
307 </assert_contents> 297 </assert_contents>
308 </output> 298 </output>
299 <output name="output_summary">
300 <assert_contents>
301 <has_text text="Stacks Statistics" />
302 </assert_contents>
303 </output>
309 304
310 <!-- catalog --> 305 <!-- catalog -->
311 <output name="catalogsnps"> 306 <output name="catalogsnps">
312 <assert_contents> 307 <assert_contents>
313 <has_text text="catalog generated" /> 308 <has_text text="catalog generated" />
393 <output name="output_log"> 388 <output name="output_log">
394 <assert_contents> 389 <assert_contents>
395 <has_text text="ref_map.pl completed" /> 390 <has_text text="ref_map.pl completed" />
396 </assert_contents> 391 </assert_contents>
397 </output> 392 </output>
393 <output name="output_summary">
394 <assert_contents>
395 <has_text text="Stacks Statistics" />
396 </assert_contents>
397 </output>
398 398
399 <!-- catalog --> 399 <!-- catalog -->
400 <output name="catalogtags"> 400 <output name="catalogtags">
401 <assert_contents> 401 <assert_contents>
402 <has_text text="catalog generated on" /> 402 <has_text text="catalog generated on" />