Mercurial > repos > iuc > stacks2_tsv2bam
comparison stacks_tsv2bam.xml @ 2:bf0e43ab0416 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author | iuc |
---|---|
date | Wed, 15 Jul 2020 17:29:50 -0400 |
parents | 8c2617661c49 |
children | 69842dd5aa48 |
comparison
equal
deleted
inserted
replaced
1:8c2617661c49 | 2:bf0e43ab0416 |
---|---|
54 <expand macro="input_stacks_macro"/> | 54 <expand macro="input_stacks_macro"/> |
55 <expand macro="input_cat_macro"/> | 55 <expand macro="input_cat_macro"/> |
56 <expand macro="input_matches_macro"/> | 56 <expand macro="input_matches_macro"/> |
57 <!-- TODO add BAM? --> | 57 <!-- TODO add BAM? --> |
58 <expand macro="fastq_input" fastq_optional="true" se_option="reverse reads" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam. Leave selection empty if you analyse single end data."/> | 58 <expand macro="fastq_input" fastq_optional="true" se_option="reverse reads" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam. Leave selection empty if you analyse single end data."/> |
59 <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" /> | 59 <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"/> |
60 <expand macro="in_log"/> | 60 <expand macro="in_log"/> |
61 </inputs> | 61 </inputs> |
62 | 62 |
63 <outputs> | 63 <outputs> |
64 <expand macro="out_log"/> | 64 <expand macro="out_log"/> |
65 <expand macro="tsv2bam_outputs_macro"/> | 65 <expand macro="tsv2bam_outputs_macro"/> |
66 </outputs> | 66 </outputs> |
67 | 67 |
68 <tests> | 68 <tests> |
69 <!-- test wo paired end data --> | 69 <!-- test wo paired end data --> |
70 <test> | 70 <test expect_num_outputs="2"> |
71 <param name="input_cat"> | 71 <param name="input_cat"> |
72 <collection type="list"> | 72 <collection type="list"> |
73 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> | 73 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> |
74 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> | 74 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> |
75 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> | 75 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/> |
76 </collection> | 76 </collection> |
77 </param> | 77 </param> |
78 <param name="input_stacks"> | 78 <param name="input_stacks"> |
79 <collection type="list"> | 79 <collection type="list"> |
80 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> | 80 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/> |
81 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> | 81 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/> |
82 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> | 82 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/> |
83 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> | 83 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/> |
84 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" /> | 84 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/> |
85 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" /> | 85 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/> |
86 </collection> | 86 </collection> |
87 </param> | 87 </param> |
88 <param name="input_matches"> | 88 <param name="input_matches"> |
89 <collection type="list"> | 89 <collection type="list"> |
90 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" /> | 90 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> |
91 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" /> | 91 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> |
92 </collection> | 92 </collection> |
93 </param> | 93 </param> |
94 <param name="add_log" value="yes" /> | 94 <param name="add_log" value="yes"/> |
95 <output name="output_log" ftype="txt" file="tsv2bam/tsv2bam.log" lines_diff="14"/> | 95 <output name="output_log" ftype="txt" file="tsv2bam/tsv2bam.log" lines_diff="14"/> |
96 <output_collection name="bams" type="list" count="2"> | 96 <output_collection name="bams" type="list" count="2"> |
97 <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/> | 97 <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/> |
98 <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/> | 98 <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/> |
99 </output_collection> | 99 </output_collection> |
100 </test> | 100 </test> |
101 <!-- test w popmap, w reverse reads as multiple selection --> | 101 <!-- test w popmap, w reverse reads as multiple selection --> |
102 <test> | 102 <test expect_num_outputs="2"> |
103 <param name="input_cat"> | 103 <param name="input_cat"> |
104 <collection type="list"> | 104 <collection type="list"> |
105 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> | 105 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> |
106 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> | 106 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> |
107 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> | 107 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/> |
108 </collection> | 108 </collection> |
109 </param> | 109 </param> |
110 <param name="input_stacks"> | 110 <param name="input_stacks"> |
111 <collection type="list"> | 111 <collection type="list"> |
112 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> | 112 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/> |
113 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> | 113 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/> |
114 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> | 114 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/> |
115 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> | 115 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/> |
116 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" /> | 116 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/> |
117 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" /> | 117 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/> |
118 </collection> | 118 </collection> |
119 </param> | 119 </param> |
120 <param name="input_matches"> | 120 <param name="input_matches"> |
121 <collection type="list"> | 121 <collection type="list"> |
122 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" /> | 122 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> |
123 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" /> | 123 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> |
124 </collection> | 124 </collection> |
125 </param> | 125 </param> |
126 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> | 126 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> |
127 <param name="input_type|input_type_select" value="single"/> | 127 <param name="input_type|input_type_select" value="single"/> |
128 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger" /> | 128 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> |
129 <param name="add_log" value="yes" /> | 129 <param name="add_log" value="yes"/> |
130 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> | 130 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> |
131 <output_collection name="bams" type="list" count="2"/> | 131 <output_collection name="bams" type="list" count="2"/> |
132 </test> | 132 </test> |
133 <!-- test w reverse reads as list --> | 133 <!-- test w reverse reads as list --> |
134 <test> | 134 <test expect_num_outputs="2"> |
135 <param name="input_cat"> | 135 <param name="input_cat"> |
136 <collection type="list"> | 136 <collection type="list"> |
137 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> | 137 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> |
138 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> | 138 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> |
139 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> | 139 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/> |
140 </collection> | 140 </collection> |
141 </param> | 141 </param> |
142 <param name="input_stacks"> | 142 <param name="input_stacks"> |
143 <collection type="list"> | 143 <collection type="list"> |
144 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> | 144 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/> |
145 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> | 145 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/> |
146 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> | 146 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/> |
147 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> | 147 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/> |
148 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" /> | 148 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/> |
149 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" /> | 149 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/> |
150 </collection> | 150 </collection> |
151 </param> | 151 </param> |
152 <param name="input_matches"> | 152 <param name="input_matches"> |
153 <collection type="list"> | 153 <collection type="list"> |
154 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" /> | 154 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> |
155 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" /> | 155 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> |
156 </collection> | 156 </collection> |
157 </param> | 157 </param> |
158 <param name="input_type|input_type_select" value="paired"/> | 158 <param name="input_type|input_type_select" value="paired"/> |
159 <param name="input_type|fqinputs"> | 159 <param name="input_type|fqinputs"> |
160 <collection type="list"> | 160 <collection type="list"> |
161 <element name="PopA_01" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger" /> | 161 <element name="PopA_01" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/> |
162 <element name="PopA_02" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> | 162 <element name="PopA_02" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> |
163 </collection> | 163 </collection> |
164 </param> | 164 </param> |
165 <param name="add_log" value="yes" /> | 165 <param name="add_log" value="yes"/> |
166 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> | 166 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> |
167 <output_collection name="bams" type="list" count="2"/> | 167 <output_collection name="bams" type="list" count="2"/> |
168 </test> | 168 </test> |
169 <!-- test w paired reads as paired dataset list --> | 169 <!-- test w paired reads as paired dataset list --> |
170 <test> | 170 <test expect_num_outputs="2"> |
171 <param name="input_cat"> | 171 <param name="input_cat"> |
172 <collection type="list"> | 172 <collection type="list"> |
173 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> | 173 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> |
174 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> | 174 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> |
175 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> | 175 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/> |
176 </collection> | 176 </collection> |
177 </param> | 177 </param> |
178 <param name="input_stacks"> | 178 <param name="input_stacks"> |
179 <collection type="list"> | 179 <collection type="list"> |
180 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> | 180 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/> |
181 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> | 181 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/> |
182 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> | 182 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/> |
183 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> | 183 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/> |
184 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" /> | 184 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/> |
185 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" /> | 185 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/> |
186 </collection> | 186 </collection> |
187 </param> | 187 </param> |
188 <param name="input_matches"> | 188 <param name="input_matches"> |
189 <collection type="list"> | 189 <collection type="list"> |
190 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" /> | 190 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> |
191 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" /> | 191 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> |
192 </collection> | 192 </collection> |
193 </param> | 193 </param> |
194 <param name="input_type|input_type_select" value="paired"/> | 194 <param name="input_type|input_type_select" value="paired"/> |
195 <param name="input_type|fqinputs"> | 195 <param name="input_type|fqinputs"> |
196 <collection type="list:paired"> | 196 <collection type="list:paired"> |
197 <element name="PopA_01"> | 197 <element name="PopA_01"> |
198 <collection type="paired"> | 198 <collection type="paired"> |
199 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> | 199 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/> |
200 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/> | 200 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/> |
201 </collection> | 201 </collection> |
202 </element> | 202 </element> |
203 <element name="PopA_02"> | 203 <element name="PopA_02"> |
204 <collection type="paired"> | 204 <collection type="paired"> |
205 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> | 205 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> |
206 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> | 206 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> |
207 </collection> | 207 </collection> |
208 </element> | 208 </element> |
209 </collection> | 209 </collection> |
210 </param> | 210 </param> |
211 <param name="add_log" value="yes" /> | 211 <param name="add_log" value="yes"/> |
212 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> | 212 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> |
213 <output_collection name="bams" type="list" count="2"/> | 213 <output_collection name="bams" type="list" count="2"/> |
214 </test> | 214 </test> |
215 </tests> | 215 </tests> |
216 | 216 |
217 <help> | 217 <help> |
249 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ | 249 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
250 | 250 |
251 @STACKS_INFOS@ | 251 @STACKS_INFOS@ |
252 ]]> | 252 ]]> |
253 </help> | 253 </help> |
254 <expand macro="citation" /> | 254 <expand macro="citation"/> |
255 </tool> | 255 </tool> |