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comparison stacks_cstacks.xml @ 8:759ba5c7faca 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 04:18:23 -0400
parents a62f7e799494
children be3df81c0353
comparison
equal deleted inserted replaced
7:c541e62d6c56 8:759ba5c7faca
11 mkdir stacks_inputs stacks_outputs 11 mkdir stacks_inputs stacks_outputs
12 12
13 && 13 &&
14 14
15 #set $samples = "" 15 #set $samples = ""
16 #for $input_file in $input_col: 16 #for $input_file in $input_col
17 #set $filename = str($input_file.element_identifier) 17 #set $filename = str($input_file.element_identifier)
18 #if not filename.endswith('.tsv'): 18 #if not filename.endswith('.tsv')
19 #set $filename = $filename + ".tsv" 19 #set $filename = $filename + ".tsv"
20 #end if 20 #end if
21 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename): 21 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
22 ln -s "${input_file}" "stacks_inputs/$filename" && 22 ln -s '${input_file}' 'stacks_inputs/$filename' &&
23 23
24 #if $filename.endswith('.tags.tsv'): 24 #if $filename.endswith('.tags.tsv')
25 #set samples += " -s \"stacks_inputs/" + $filename[:-9] + "\"" 25 #set samples += " -s 'stacks_inputs/" + $filename[:-9] + "'"
26 #end if 26 #end if
27 #end if 27 #end if
28 #end for 28 #end for
29 29
30 cstacks 30 cstacks
31
32 -p \${GALAXY_SLOTS:-1}
33
34 $samples
35 31
36 ## Batch description 32 ## Batch description
37 -b 1 33 -b 1
38 34
35 -p \${GALAXY_SLOTS:-1}
36
37 #if $popmap
38 -P stacks_inputs -M '$popmap'
39 #else
40 $samples
41 -o stacks_outputs
42 #end if
43
39 $g 44 $g
40 45
41 -n $n 46 -n $n
42 47
43 $include_multiple 48 $include_multiple
44 49
45 #if $gapped.use_gapped: 50 #if $gapped.use_gapped == "yes"
46 --gapped 51 --gapped
47 --max_gaps $gapped.max_gaps 52 --max_gaps $gapped.max_gaps
48 --min_aln_len $gapped.min_aln_len 53 --min_aln_len $gapped.min_aln_len
49 #end if 54 #end if
50 55
51 -o stacks_outputs 56 2>&1 | tee cstacks.log
52 57
53 > cstacks.log 2>&1 58 #if $popmap
59 ## When using a popmap, stacks write to the input dir
60 && mv stacks_inputs/batch_1.catalog.*.tsv stacks_outputs/
61 #end if
62
63 &&
64
65 stacks_summary.py --stacks-prog cstacks --res-dir stacks_outputs --logfile cstacks.log --summary stacks_outputs/summary.html
54 ]]></command> 66 ]]></command>
55 67
56 <inputs> 68 <inputs>
57 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map, refmap, ustacks or pstacks)" /> 69 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map, refmap, ustacks or pstacks)" />
58 70
71 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, the catalog will be built from samples listed in this file" optional="true" argument="-M" />
72
59 <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" /> 73 <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />
60 74
61 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample tags when building the catalog"/> 75 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample tags when building the catalog"/>
62 76
63 <param name="include_multiple" argument="-m" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Include tags in the catalog that match to more than one entry" /> 77 <param name="include_multiple" argument="-m" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Include tags in the catalog that match to more than one entry" />
64 78
65 <conditional name="gapped"> 79 <conditional name="gapped">
66 <param name="use_gapped" argument="--gapped" type="boolean" checked="false" label="Perform gapped alignments between stacks" /> 80 <param name="use_gapped" argument="--gapped" type="select" label="Perform gapped alignments between stacks">
67 <when value="false"></when> 81 <option value="no" selected="true">No</option>
68 <when value="true"> 82 <option value="yes">Yes</option>
83 </param>
84 <when value="no"/>
85 <when value="yes">
69 <param name="max_gaps" argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/> 86 <param name="max_gaps" argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/>
70 <param name="min_aln_len" argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/> 87 <param name="min_aln_len" argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/>
71 </when> 88 </when>
72 </conditional> 89 </conditional>
73 </inputs> 90 </inputs>
74 91
75 <outputs> 92 <outputs>
76 <data format="txt" name="output_log" label="cstacks.log with ${tool.name} on ${on_string}" from_work_dir="cstacks.log" /> 93 <data format="txt" name="output_log" label="cstacks.log with ${tool.name} on ${on_string}" from_work_dir="cstacks.log" />
94
95 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
77 96
78 <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" /> 97 <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" />
79 <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" /> 98 <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" />
80 <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" /> 99 <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" />
81 </outputs> 100 </outputs>
101 <output name="output_log"> 120 <output name="output_log">
102 <assert_contents> 121 <assert_contents>
103 <has_text text="done." /> 122 <has_text text="done." />
104 </assert_contents> 123 </assert_contents>
105 </output> 124 </output>
125 <output name="output_summary">
126 <assert_contents>
127 <has_text text="Stacks Statistics" />
128 </assert_contents>
129 </output>
106 130
107 <!-- catalog --> 131 <!-- catalog -->
108 <output name="catalogtags"> 132 <output name="catalogtags">
109 <assert_contents> 133 <assert_contents>
110 <has_text text="catalog generated on" /> 134 <has_text text="catalog generated on" />
136 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" /> 160 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
137 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" /> 161 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
138 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" /> 162 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
139 </collection> 163 </collection>
140 </param> 164 </param>
141 <param name="gapped|use_gapped" value="true" /> 165 <param name="gapped|use_gapped" value="yes" />
142 166
143 <output name="output_log"> 167 <output name="output_log">
144 <assert_contents> 168 <assert_contents>
145 <has_text text="done." /> 169 <has_text text="done." />
170 </assert_contents>
171 </output>
172 <output name="output_summary">
173 <assert_contents>
174 <has_text text="Stacks Statistics" />
175 </assert_contents>
176 </output>
177
178 <!-- catalog -->
179 <output name="catalogtags">
180 <assert_contents>
181 <has_text text="catalog generated on" />
182 </assert_contents>
183 </output>
184 <output name="catalogsnps">
185 <assert_contents>
186 <has_text text="catalog generated on" />
187 </assert_contents>
188 </output>
189 <output name="catalogalleles">
190 <assert_contents>
191 <has_text text="catalog generated on" />
192 </assert_contents>
193 </output>
194 </test>
195
196 <test>
197 <param name="input_col">
198 <collection type="list">
199 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
200 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
201 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
202 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
203 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
204 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
205 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
206 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
207 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
208 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
209 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
210 </collection>
211 </param>
212
213 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
214
215 <output name="output_log">
216 <assert_contents>
217 <has_text text="done." />
218 </assert_contents>
219 </output>
220 <output name="output_summary">
221 <assert_contents>
222 <has_text text="Stacks Statistics" />
146 </assert_contents> 223 </assert_contents>
147 </output> 224 </output>
148 225
149 <!-- catalog --> 226 <!-- catalog -->
150 <output name="catalogtags"> 227 <output name="catalogtags">