Mercurial > repos > iuc > stacks_sstacks

comparison stacks_sstacks.xml @ 8:db683c98e455 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 04:17:14 -0400
parents 679f97ac0dd5
children 563af4497055
comparison
equal deleted inserted replaced
7:b185c3e3f1dc 8:db683c98e455
11 mkdir stacks_inputs stacks_outputs 11 mkdir stacks_inputs stacks_outputs
12 12
13 && 13 &&
14 14
15 #set $catalog = "" 15 #set $catalog = ""
16 #for $input_file in $input_cat: 16 #for $input_file in $input_cat
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 = $filename + ".tsv"
20 #end if 20 #end if
21 #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename): 21 #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
22 ln -s "${input_file}" "stacks_inputs/$filename" && 22 ln -s '${input_file}' 'stacks_inputs/$filename' &&
23 23
24 #if $filename.endswith('.tags.tsv'): 24 #if $filename.endswith('.tags.tsv')
25 #set catalog += " -c \"stacks_inputs/"+$filename[:-17] + "\"" 25 #set catalog += " -c 'stacks_inputs/"+$filename[:-17] + "'"
26 #end if 26 #end if
27 #end if 27 #end if
28 #end for 28 #end for
29 29
30 #set $samples = "" 30 #set $samples = ""
31 #for $input_file in $input_tags: 31 #for $input_file in $input_tags
32 #set $filename = str($input_file.element_identifier) 32 #set $filename = str($input_file.element_identifier)
33 #if not filename.endswith('.tsv'): 33 #if not filename.endswith('.tsv')
34 #set $filename = $filename + ".tsv" 34 #set $filename = $filename + ".tsv"
35 #end if 35 #end if
36 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename): 36 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
37 ln -s "${input_file}" "stacks_inputs/$filename" && 37 ln -s '${input_file}' 'stacks_inputs/$filename' &&
38 38
39 #if $filename.endswith('.tags.tsv'): 39 #if $filename.endswith('.tags.tsv')
40 #set samples += " -s \"stacks_inputs/"+$filename[:-9] + "\"" 40 #set samples += " -s 'stacks_inputs/"+$filename[:-9] + "'"
41 #end if 41 #end if
42 #end if 42 #end if
43 #end for 43 #end for
44 44
45 sstacks 45 sstacks
46
47 -p \${GALAXY_SLOTS:-1}
48
49 $catalog
50
51 $samples
52 46
53 ## Batch description 47 ## Batch description
54 -b 1 48 -b 1
55 49
50 -p \${GALAXY_SLOTS:-1}
51
52 #if $popmap
53 -P stacks_inputs -M '$popmap'
54 #else
55 $catalog
56 $samples
57 -o stacks_outputs
58 #end if
59
56 $g 60 $g
57 61
58 $check_haplo 62 $check_haplo
59 63
60 $gapped 64 $gapped
61 65
62 -o stacks_outputs 66 2>&1 | tee sstacks.log
63 67
64 > sstacks.log 2>&1 68 #if $popmap
69 ## When using a popmap, stacks write to the input dir
70 && mv stacks_inputs/*matches.tsv stacks_outputs/
71 #end if
72
73 &&
74
75 stacks_summary.py --stacks-prog sstacks --res-dir stacks_outputs --logfile sstacks.log --summary stacks_outputs/summary.html
65 ]]></command> 76 ]]></command>
66 77
67 <inputs> 78 <inputs>
68 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" /> 79 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" />
69 <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks/pstacks" /> 80 <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks/pstacks" />
70 81
82 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" />
83
71 <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" /> 84 <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />
72 85
73 <param name="check_haplo" argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Don't verify haplotype of matching locus" /> 86 <param name="check_haplo" argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Don't verify haplotype of matching locus" />
74 87
75 <param name="gapped" argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" /> 88 <param name="gapped" argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" />
76 </inputs> 89 </inputs>
77 90
78 <outputs> 91 <outputs>
79 <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" /> 92 <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" />
93
94 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
80 95
81 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}"> 96 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
82 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" /> 97 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
83 </collection> 98 </collection>
84 </outputs> 99 </outputs>
108 <output name="output_log"> 123 <output name="output_log">
109 <assert_contents> 124 <assert_contents>
110 <has_text text="Outputing to file" /> 125 <has_text text="Outputing to file" />
111 </assert_contents> 126 </assert_contents>
112 </output> 127 </output>
128 <output name="output_summary">
129 <assert_contents>
130 <has_text text="Stacks Statistics" />
131 </assert_contents>
132 </output>
113 133
114 <output_collection name="matches"> 134 <output_collection name="matches">
115 <element name="PopA_01.matches"> 135 <element name="PopA_01.matches">
116 <assert_contents> 136 <assert_contents>
117 <has_text text="generated on " /> 137 <has_text text="generated on " />
144 <param name="check_haplo" value="true" /> 164 <param name="check_haplo" value="true" />
145 165
146 <output name="output_log"> 166 <output name="output_log">
147 <assert_contents> 167 <assert_contents>
148 <has_text text="Outputing to file" /> 168 <has_text text="Outputing to file" />
169 </assert_contents>
170 </output>
171 <output name="output_summary">
172 <assert_contents>
173 <has_text text="Stacks Statistics" />
174 </assert_contents>
175 </output>
176
177 <output_collection name="matches">
178 <element name="PopA_01.matches">
179 <assert_contents>
180 <has_text text="generated on " />
181 </assert_contents>
182 </element>
183 </output_collection>
184 </test>
185
186 <test>
187 <param name="input_cat">
188 <collection type="list">
189 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
190 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
191 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
192 </collection>
193 </param>
194 <param name="input_tags">
195 <collection type="list">
196 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
197 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
198 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
199 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
200 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
201 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
202 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
203 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
204 </collection>
205 </param>
206
207 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
208
209 <output name="output_log">
210 <assert_contents>
211 <has_text text="Outputing to file" />
212 </assert_contents>
213 </output>
214 <output name="output_summary">
215 <assert_contents>
216 <has_text text="Stacks Statistics" />
149 </assert_contents> 217 </assert_contents>
150 </output> 218 </output>
151 219
152 <output_collection name="matches"> 220 <output_collection name="matches">
153 <element name="PopA_01.matches"> 221 <element name="PopA_01.matches">