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 |
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| 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> |