Mercurial > repos > iuc > stacks2_procrad
comparison stacks_procrad.xml @ 2:bd5ff77e2036 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
| author | iuc |
|---|---|
| date | Wed, 15 Jul 2020 17:33:16 -0400 |
| parents | ca7aa77c7f57 |
| children | b4bab607eb05 |
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| 1:ca7aa77c7f57 | 2:bd5ff77e2036 |
|---|---|
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 8 <expand macro="version_cmd"/> | 8 <expand macro="version_cmd"/> |
| 9 <command detect_errors="aggressive"><![CDATA[ | 9 <command detect_errors="aggressive"><![CDATA[ |
| 10 @FASTQ_INPUT_FUNCTIONS@ | 10 @FASTQ_INPUT_FUNCTIONS@ |
| 11 | |
| 12 python '$__tool_directory__'/check_bcfile.py '$barcode' && | |
| 13 | |
| 11 mkdir stacks_inputs stacks_outputs && | 14 mkdir stacks_inputs stacks_outputs && |
| 12 | 15 |
| 13 #if $output_log | 16 #if $output_log |
| 14 ln -s '$output_log' stacks_outputs/process_radtags.stacks_inputs.log && | 17 ln -s '$output_log' stacks_outputs/process_radtags.stacks_inputs.log && |
| 15 #end if | 18 #end if |
| 67 </when> | 70 </when> |
| 68 </conditional> | 71 </conditional> |
| 69 | 72 |
| 70 <section name="options_advanced" title="advanced options" expanded="False"> | 73 <section name="options_advanced" title="advanced options" expanded="False"> |
| 71 <expand macro="common_advanced"/> | 74 <expand macro="common_advanced"/> |
| 72 <param argument="--bestrad" type="boolean" checked="false" truevalue="--bestrad" falsevalue="" label="Library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads" /> | 75 <param argument="--bestrad" type="boolean" checked="false" truevalue="--bestrad" falsevalue="" label="Library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads"/> |
| 73 <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="Disable checking if the RAD site is intact" /> | 76 <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="Disable checking if the RAD site is intact"/> |
| 74 <expand macro="rescue_barcode"/> | 77 <expand macro="rescue_barcode"/> |
| 75 <expand macro="process_adapter"/> | 78 <expand macro="process_adapter"/> |
| 76 </section> | 79 </section> |
| 77 | 80 |
| 78 <expand macro="process_filter"/> | 81 <expand macro="process_filter"/> |
| 84 <expand macro="out_log"/> | 87 <expand macro="out_log"/> |
| 85 <expand macro="process_outputs"/> | 88 <expand macro="process_outputs"/> |
| 86 </outputs> | 89 </outputs> |
| 87 <tests> | 90 <tests> |
| 88 <!-- single single ended input, no filtering (hence no capturing) + log --> | 91 <!-- single single ended input, no filtering (hence no capturing) + log --> |
| 89 <test> | 92 <test expect_num_outputs="2"> |
| 90 <param name="input_type|input_type_select" value="single"/> | 93 <param name="input_type|input_type_select" value="single"/> |
| 91 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> | 94 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> |
| 92 <param name="input_type|barcode_encoding" value="--inline_null"/> | 95 <param name="input_type|barcode_encoding" value="--inline_null"/> |
| 93 <param name="barcode" value="procrad/barcodes"/> | 96 <param name="barcode" value="procrad/barcodes"/> |
| 94 <param name="options_enzyme|options_enzyme_selector" value="1"/> | 97 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
| 95 <param name="options_enzyme|enzyme" value="ecoRI"/> | 98 <param name="options_enzyme|enzyme" value="ecoRI"/> |
| 96 <param name="add_log" value="yes" /> | 99 <param name="add_log" value="yes"/> |
| 97 <output name="output_log" file="procrad/process_radtags.out" lines_diff="4"/> | 100 <output name="output_log" file="procrad/process_radtags.out" lines_diff="4"/> |
| 98 <output_collection name="demultiplexed" count="40"> | 101 <output_collection name="demultiplexed" count="40"> |
| 99 <element name="PopA_01" file="demultiplexed/PopA_01.fq" ftype="fastqsanger" /> | 102 <element name="PopA_01" file="demultiplexed/PopA_01.fq" ftype="fastqsanger"/> |
| 100 </output_collection> | 103 </output_collection> |
| 101 </test> | 104 </test> |
| 102 <!-- multiple (zipped) single end input (misusing R2 as add single end read file), | 105 <!-- multiple (zipped) single end input (misusing R2 as add single end read file), |
| 103 discarding by quality and capturing them --> | 106 discarding by quality and capturing them --> |
| 104 <test> | 107 <test expect_num_outputs="3"> |
| 105 <param name="input_type|input_type_select" value="single"/> | 108 <param name="input_type|input_type_select" value="single"/> |
| 106 <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip,procrad/R2.fq.gzip"/> | 109 <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip,procrad/R2.fq.gzip"/> |
| 107 <param name="input_type|barcode_encoding" value="--inline_null"/> | 110 <param name="input_type|barcode_encoding" value="--inline_null"/> |
| 108 <param name="barcode" value="procrad/barcodes"/> | 111 <param name="barcode" value="procrad/barcodes"/> |
| 109 <param name="options_enzyme|options_enzyme_selector" value="1"/> | 112 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
| 110 <param name="options_enzyme|enzyme" value="ecoRI"/> | 113 <param name="options_enzyme|enzyme" value="ecoRI"/> |
| 111 <param name="filter_cond|filter_select" value="yes"/> | 114 <param name="filter_cond|filter_select" value="yes"/> |
| 112 <param name="filter_cond|discard" value="-q"/> | 115 <param name="filter_cond|discard" value="-q"/> |
| 113 <param name="filter_cond|sliding" value="0.1" /> | 116 <param name="filter_cond|sliding" value="0.1"/> |
| 114 <param name="filter_cond|score" value="11" /> | 117 <param name="filter_cond|score" value="11"/> |
| 115 <param name="filter_cond|remove" value="-c" /> | 118 <param name="filter_cond|remove" value="-c"/> |
| 116 <param name="capture" value="-D"/> | 119 <param name="capture" value="-D"/> |
| 117 <param name="outype" value="gzfastq"/> | 120 <param name="outype" value="gzfastq"/> |
| 118 <param name="add_log" value="yes" /> | 121 <param name="add_log" value="yes"/> |
| 119 <output name="output_log" file="procrad/process_radtags2.out" lines_diff="4"/> | 122 <output name="output_log" file="procrad/process_radtags2.out" lines_diff="4"/> |
| 120 <assert_command> | 123 <assert_command> |
| 121 <has_text text="-q" /> | 124 <has_text text="-q"/> |
| 122 <has_text text="-w 0.1" /> | 125 <has_text text="-w 0.1"/> |
| 123 <has_text text="-s 11" /> | 126 <has_text text="-s 11"/> |
| 124 <has_text text="-c" /> | 127 <has_text text="-c"/> |
| 125 <has_text text="-D" /> | 128 <has_text text="-D"/> |
| 126 </assert_command> | 129 </assert_command> |
| 127 <output_collection name="demultiplexed" count="40"> | 130 <output_collection name="demultiplexed" count="40"> |
| 128 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> | 131 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> |
| 129 </output_collection> | 132 </output_collection> |
| 130 <output_collection name="discarded" count="2"> | 133 <output_collection name="discarded" count="2"> |
| 131 <element name="R1" file="procrad/R1.fq.discards" ftype="fastqsanger"/> | 134 <element name="R1" file="procrad/R1.fq.discards" ftype="fastqsanger"/> |
| 132 <element name="R2" file="procrad/R2.fq.discards" ftype="fastqsanger"/> | 135 <element name="R2" file="procrad/R2.fq.discards" ftype="fastqsanger"/> |
| 133 </output_collection> | 136 </output_collection> |
| 134 </test> | 137 </test> |
| 135 <!-- paired input, no quality but length filter, gzfasta output --> | 138 <!-- paired input, no quality but length filter, gzfasta output --> |
| 136 <test> | 139 <test expect_num_outputs="4"> |
| 137 <param name="input_type|input_type_select" value="paired"/> | 140 <param name="input_type|input_type_select" value="paired"/> |
| 138 <param name="input_type|fqinputs"> | 141 <param name="input_type|fqinputs"> |
| 139 <collection type="list:paired"> | 142 <collection type="list:paired"> |
| 140 <element name="reads"> | 143 <element name="reads"> |
| 141 <collection type="paired"> | 144 <collection type="paired"> |
| 142 <element name="forward" value="procrad/R1.fq" ftype="fastqsanger" /> | 145 <element name="forward" value="procrad/R1.fq" ftype="fastqsanger"/> |
| 143 <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/> | 146 <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/> |
| 144 </collection> | 147 </collection> |
| 145 </element> | 148 </element> |
| 146 </collection> | 149 </collection> |
| 147 </param> | 150 </param> |
| 150 <param name="options_enzyme|enzyme" value="ecoRI"/> | 153 <param name="options_enzyme|enzyme" value="ecoRI"/> |
| 151 <param name="filter_cond|filter_select" value="no"/> | 154 <param name="filter_cond|filter_select" value="no"/> |
| 152 <param name="filter_cond|len_limit" value="50"/> | 155 <param name="filter_cond|len_limit" value="50"/> |
| 153 <param name="capture" value="-D"/> | 156 <param name="capture" value="-D"/> |
| 154 <param name="outype" value="gzfasta"/> | 157 <param name="outype" value="gzfasta"/> |
| 155 <param name="add_log" value="yes" /> | 158 <param name="add_log" value="yes"/> |
| 156 <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/> | 159 <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/> |
| 157 <assert_command> | 160 <assert_command> |
| 158 <has_text text="--len_limit 50" /> | 161 <has_text text="--len_limit 50"/> |
| 159 </assert_command> | 162 </assert_command> |
| 160 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> | 163 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> |
| 161 <element name="PopA_01"> | 164 <element name="PopA_01"> |
| 162 <element name="forward" value="demultiplexed/PopA_01.1.fa.gz" ftype="fasta.gz" /> | 165 <element name="forward" value="demultiplexed/PopA_01.1.fa.gz" ftype="fasta.gz"/> |
| 163 <element name="reverse" value="demultiplexed/PopA_01.2.fa.gz" ftype="fasta.gz" /> | 166 <element name="reverse" value="demultiplexed/PopA_01.2.fa.gz" ftype="fasta.gz"/> |
| 164 </element> | 167 </element> |
| 165 </output_collection> | 168 </output_collection> |
| 166 <output_collection name="remaining" type="list:paired" count="40"> | 169 <output_collection name="remaining" type="list:paired" count="40"> |
| 167 <element name="PopA_01"> | 170 <element name="PopA_01"> |
| 168 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa.gz" ftype="fasta.gz"/> | 171 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa.gz" ftype="fasta.gz"/> |
| 175 <element name="reverse" file="procrad/R2.fa.discards" ftype="fasta"/> | 178 <element name="reverse" file="procrad/R2.fa.discards" ftype="fasta"/> |
| 176 </element> | 179 </element> |
| 177 </output_collection> | 180 </output_collection> |
| 178 </test> | 181 </test> |
| 179 <!-- paired input (gzipped) + advanced options + two enzymes, fasta output --> | 182 <!-- paired input (gzipped) + advanced options + two enzymes, fasta output --> |
| 180 <test> | 183 <test expect_num_outputs="3"> |
| 181 <param name="input_type|input_type_select" value="paired"/> | 184 <param name="input_type|input_type_select" value="paired"/> |
| 182 <param name="input_type|fqinputs"> | 185 <param name="input_type|fqinputs"> |
| 183 <collection type="list:paired"> | 186 <collection type="list:paired"> |
| 184 <element name="reads"> | 187 <element name="reads"> |
| 185 <collection type="paired"> | 188 <collection type="paired"> |
| 186 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz" /> | 189 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz"/> |
| 187 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/> | 190 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/> |
| 188 </collection> | 191 </collection> |
| 189 </element> | 192 </element> |
| 190 </collection> | 193 </collection> |
| 191 </param> | 194 </param> |
| 192 <param name="barcode" value="procrad/barcodes"/> | 195 <param name="barcode" value="procrad/barcodes"/> |
| 193 <param name="options_enzyme|options_enzyme_selector" value="2"/> | 196 <param name="options_enzyme|options_enzyme_selector" value="2"/> |
| 194 <param name="options_enzyme|enzyme" value="ecoRI"/> | 197 <param name="options_enzyme|enzyme" value="ecoRI"/> |
| 195 <param name="options_enzyme|enzyme2" value="ecoRI"/> | 198 <param name="options_enzyme|enzyme2" value="ecoRI"/> |
| 196 <param name="options_advanced|truncate" value="70" /> | 199 <param name="options_advanced|truncate" value="70"/> |
| 197 <param name="options_advanced|rescue_cond|rescue" value="-r"/> | 200 <param name="options_advanced|rescue_cond|rescue" value="-r"/> |
| 198 <param name="options_advanced|rescue_cond|barcode_dist_1" value="2" /> | 201 <param name="options_advanced|rescue_cond|barcode_dist_1" value="2"/> |
| 199 <param name="options_advanced|rescue_cond|barcode_dist_2" value="2" /> | 202 <param name="options_advanced|rescue_cond|barcode_dist_2" value="2"/> |
| 200 <param name="options_advanced|bestrad" value="--bestrad" /> | 203 <param name="options_advanced|bestrad" value="--bestrad"/> |
| 201 <param name="options_advanced|retain_header" value="--retain_header"/> | 204 <param name="options_advanced|retain_header" value="--retain_header"/> |
| 202 <param name="options_advanced|disable_rad_check" value="--disable_rad_check" /> | 205 <param name="options_advanced|disable_rad_check" value="--disable_rad_check"/> |
| 203 <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" /> | 206 <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/> |
| 204 <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" /> | 207 <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"/> |
| 205 <param name="options_advanced|adapter_mm" value="2" /> | 208 <param name="options_advanced|adapter_mm" value="2"/> |
| 206 <param name="outype" value="fasta"/> | 209 <param name="outype" value="fasta"/> |
| 207 <assert_command> | 210 <assert_command> |
| 208 <has_text text="-e ecoRI" /> | 211 <has_text text="-e ecoRI"/> |
| 209 <has_text text="--renz_2 ecoRI" /> | 212 <has_text text="--renz_2 ecoRI"/> |
| 210 <has_text text="-t 70" /> | 213 <has_text text="-t 70"/> |
| 211 <has_text text="-r" /> | 214 <has_text text="-r"/> |
| 212 <has_text text="--bestrad" /> | 215 <has_text text="--bestrad"/> |
| 213 <has_text text="--retain_header" /> | 216 <has_text text="--retain_header"/> |
| 214 <has_text text="--disable_rad_check" /> | 217 <has_text text="--disable_rad_check"/> |
| 215 <has_text text="--barcode_dist_1 2" /> | 218 <has_text text="--barcode_dist_1 2"/> |
| 216 <has_text text="--barcode_dist_2 2" /> | 219 <has_text text="--barcode_dist_2 2"/> |
| 217 <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" /> | 220 <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/> |
| 218 <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" /> | 221 <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"/> |
| 219 <has_text text="--adapter_mm 2" /> | 222 <has_text text="--adapter_mm 2"/> |
| 220 </assert_command> | 223 </assert_command> |
| 221 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> | 224 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> |
| 222 <element name="PopA_01"> | 225 <element name="PopA_01"> |
| 223 <element name="forward" file="demultiplexed/PopA_01.1.fa" ftype="fasta"/> | 226 <element name="forward" file="demultiplexed/PopA_01.1.fa" ftype="fasta"/> |
| 224 <element name="reverse" file="demultiplexed/PopA_01.2.fa" ftype="fasta"/> | 227 <element name="reverse" file="demultiplexed/PopA_01.2.fa" ftype="fasta"/> |
| 225 </element> | 228 </element> |
| 226 </output_collection> | 229 </output_collection> |
| 227 <output_collection name="remaining" type="list:paired" count="40"> | 230 <output_collection name="remaining" type="list:paired" count="40"> |
| 228 <element name="PopA_01"> | 231 <element name="PopA_01"> |
| 229 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa" ftype="fasta" /> | 232 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa" ftype="fasta"/> |
| 230 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa" ftype="fasta" /> | 233 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa" ftype="fasta"/> |
| 231 </element> | 234 </element> |
| 232 </output_collection> | 235 </output_collection> |
| 236 </test> | |
| 237 <!-- test invalid barcode file --> | |
| 238 <test expect_failure="true"> | |
| 239 <param name="input_type|input_type_select" value="single"/> | |
| 240 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> | |
| 241 <param name="input_type|barcode_encoding" value="--inline_null"/> | |
| 242 <param name="barcode" value="procrad/barcodes-duplicate"/> | |
| 243 <param name="options_enzyme|options_enzyme_selector" value="1"/> | |
| 244 <param name="options_enzyme|enzyme" value="ecoRI"/> | |
| 245 <param name="add_log" value="yes"/> | |
| 246 </test> | |
| 247 <!-- test invalid barcode file --> | |
| 248 <test expect_failure="true"> | |
| 249 <param name="input_type|input_type_select" value="single"/> | |
| 250 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> | |
| 251 <param name="input_type|barcode_encoding" value="--inline_null"/> | |
| 252 <param name="barcode" value="procrad/barcodes-duplicate2"/> | |
| 253 <param name="options_enzyme|options_enzyme_selector" value="1"/> | |
| 254 <param name="options_enzyme|enzyme" value="ecoRI"/> | |
| 255 <param name="add_log" value="yes"/> | |
| 256 </test> | |
| 257 <!-- test invalid barcode file --> | |
| 258 <test expect_failure="true"> | |
| 259 <param name="input_type|input_type_select" value="single"/> | |
| 260 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> | |
| 261 <param name="input_type|barcode_encoding" value="--inline_null"/> | |
| 262 <param name="barcode" value="procrad/barcodes-duplicate3"/> | |
| 263 <param name="options_enzyme|options_enzyme_selector" value="1"/> | |
| 264 <param name="options_enzyme|enzyme" value="ecoRI"/> | |
| 265 <param name="add_log" value="yes"/> | |
| 233 </test> | 266 </test> |
| 234 </tests> | 267 </tests> |
| 235 | |
| 236 <help> | 268 <help> |
| 237 <![CDATA[ | 269 <![CDATA[ |
| 238 .. class:: infomark | 270 .. class:: infomark |
| 239 | 271 |
| 240 **What it does** | 272 **What it does** |
| 288 The sample name column can be omitted. Then the Barcodes are used for naming the output files. | 320 The sample name column can be omitted. Then the Barcodes are used for naming the output files. |
| 289 | 321 |
| 290 @STACKS_INFOS@ | 322 @STACKS_INFOS@ |
| 291 ]]> | 323 ]]> |
| 292 </help> | 324 </help> |
| 293 <expand macro="citation" /> | 325 <expand macro="citation"/> |
| 294 </tool> | 326 </tool> |