Mercurial > repos > iuc > stacks2_procrad
comparison stacks_procrad.xml @ 1:ca7aa77c7f57 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
| author | iuc |
|---|---|
| date | Mon, 30 Sep 2019 14:20:50 -0400 |
| parents | 9993234400f1 |
| children | bd5ff77e2036 |
comparison
equal
deleted
inserted
replaced
| 0:9993234400f1 | 1:ca7aa77c7f57 |
|---|---|
| 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 mkdir stacks_inputs stacks_outputs && | 11 mkdir stacks_inputs stacks_outputs && |
| 12 | 12 |
| 13 #if $output_log | |
| 14 ln -s '$output_log' stacks_outputs/process_radtags.stacks_inputs.log && | |
| 15 #end if | |
| 16 | |
| 13 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" ) | 17 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" ) |
| 14 $link_command | 18 $link_command |
| 15 | 19 |
| 16 process_radtags | 20 process_radtags |
| 17 | 21 |
| 35 $options_advanced.bestrad | 39 $options_advanced.bestrad |
| 36 $options_advanced.disable_rad_check | 40 $options_advanced.disable_rad_check |
| 37 | 41 |
| 38 ## Output options | 42 ## Output options |
| 39 ## --merge not implemented in Galaxy | 43 ## --merge not implemented in Galaxy |
| 40 #if $output_log | 44 |
| 41 && mv stacks_outputs/process_radtags.stacks_inputs.log $output_log | |
| 42 #end if | |
| 43 @PROCESS_FASTQ_POSTPROC@ | 45 @PROCESS_FASTQ_POSTPROC@ |
| 44 ]]></command> | 46 ]]></command> |
| 45 | 47 |
| 46 <inputs> | 48 <inputs> |
| 47 <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/> | 49 <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/> |
| 105 <param name="input_type|barcode_encoding" value="--inline_null"/> | 107 <param name="input_type|barcode_encoding" value="--inline_null"/> |
| 106 <param name="barcode" value="procrad/barcodes"/> | 108 <param name="barcode" value="procrad/barcodes"/> |
| 107 <param name="options_enzyme|options_enzyme_selector" value="1"/> | 109 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
| 108 <param name="options_enzyme|enzyme" value="ecoRI"/> | 110 <param name="options_enzyme|enzyme" value="ecoRI"/> |
| 109 <param name="filter_cond|filter_select" value="yes"/> | 111 <param name="filter_cond|filter_select" value="yes"/> |
| 110 <param name="filter_cond|discard" value="true"/> | 112 <param name="filter_cond|discard" value="-q"/> |
| 111 <param name="filter_cond|sliding" value="0.1" /> | 113 <param name="filter_cond|sliding" value="0.1" /> |
| 112 <param name="filter_cond|score" value="11" /> | 114 <param name="filter_cond|score" value="11" /> |
| 113 <param name="filter_cond|remove" value="-c" /> | 115 <param name="filter_cond|remove" value="-c" /> |
| 114 <param name="filter_cond|filter_illumina" value="--filter_illumina" /> | 116 <param name="capture" value="-D"/> |
| 115 <param name="capture" value="true"/> | |
| 116 <param name="outype" value="gzfastq"/> | 117 <param name="outype" value="gzfastq"/> |
| 118 <param name="add_log" value="yes" /> | |
| 119 <output name="output_log" file="procrad/process_radtags2.out" lines_diff="4"/> | |
| 117 <assert_command> | 120 <assert_command> |
| 118 <has_text text="-q" /> | 121 <has_text text="-q" /> |
| 119 <has_text text="-w 0.1" /> | 122 <has_text text="-w 0.1" /> |
| 120 <has_text text="-s 11" /> | 123 <has_text text="-s 11" /> |
| 121 <has_text text="-c" /> | 124 <has_text text="-c" /> |
| 122 <has_text text="--filter_illumina" /> | 125 <has_text text="-D" /> |
| 123 </assert_command> | 126 </assert_command> |
| 124 <output_collection name="demultiplexed" count="40"> | 127 <output_collection name="demultiplexed" count="40"> |
| 125 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> | 128 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> |
| 126 </output_collection> | 129 </output_collection> |
| 127 <output_collection name="discarded" count="2"> | 130 <output_collection name="discarded" count="2"> |
| 145 <param name="barcode" value="procrad/barcodes"/> | 148 <param name="barcode" value="procrad/barcodes"/> |
| 146 <param name="options_enzyme|options_enzyme_selector" value="1"/> | 149 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
| 147 <param name="options_enzyme|enzyme" value="ecoRI"/> | 150 <param name="options_enzyme|enzyme" value="ecoRI"/> |
| 148 <param name="filter_cond|filter_select" value="no"/> | 151 <param name="filter_cond|filter_select" value="no"/> |
| 149 <param name="filter_cond|len_limit" value="50"/> | 152 <param name="filter_cond|len_limit" value="50"/> |
| 150 <param name="capture" value="true"/> | 153 <param name="capture" value="-D"/> |
| 151 <param name="outype" value="gzfasta"/> | 154 <param name="outype" value="gzfasta"/> |
| 152 <param name="add_log" value="yes" /> | 155 <param name="add_log" value="yes" /> |
| 153 <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/> | 156 <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/> |
| 154 <assert_command> | 157 <assert_command> |
| 155 <has_text text="--len_limit 50" /> | 158 <has_text text="--len_limit 50" /> |
| 193 <param name="options_advanced|truncate" value="70" /> | 196 <param name="options_advanced|truncate" value="70" /> |
| 194 <param name="options_advanced|rescue_cond|rescue" value="-r"/> | 197 <param name="options_advanced|rescue_cond|rescue" value="-r"/> |
| 195 <param name="options_advanced|rescue_cond|barcode_dist_1" value="2" /> | 198 <param name="options_advanced|rescue_cond|barcode_dist_1" value="2" /> |
| 196 <param name="options_advanced|rescue_cond|barcode_dist_2" value="2" /> | 199 <param name="options_advanced|rescue_cond|barcode_dist_2" value="2" /> |
| 197 <param name="options_advanced|bestrad" value="--bestrad" /> | 200 <param name="options_advanced|bestrad" value="--bestrad" /> |
| 198 <param name="options_advanced|retain_header" value="true"/> | 201 <param name="options_advanced|retain_header" value="--retain_header"/> |
| 199 <param name="options_advanced|disable_rad_check" value="--disable_rad_check" /> | 202 <param name="options_advanced|disable_rad_check" value="--disable_rad_check" /> |
| 200 <param name="options_advanced|adapter_1" value="" /> | 203 <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" /> |
| 201 <param name="options_advanced|adapter_2" value="" /> | 204 <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" /> |
| 202 <param name="options_advanced|adapter_mm" value="" /> | 205 <param name="options_advanced|adapter_mm" value="2" /> |
| 203 <param name="outype" value="fasta"/> | 206 <param name="outype" value="fasta"/> |
| 204 <assert_command> | 207 <assert_command> |
| 205 <has_text text="-e ecoRI" /> | 208 <has_text text="-e ecoRI" /> |
| 206 <has_text text="--renz_2 ecoRI" /> | 209 <has_text text="--renz_2 ecoRI" /> |
| 207 <has_text text="-t 70" /> | 210 <has_text text="-t 70" /> |
| 209 <has_text text="--bestrad" /> | 212 <has_text text="--bestrad" /> |
| 210 <has_text text="--retain_header" /> | 213 <has_text text="--retain_header" /> |
| 211 <has_text text="--disable_rad_check" /> | 214 <has_text text="--disable_rad_check" /> |
| 212 <has_text text="--barcode_dist_1 2" /> | 215 <has_text text="--barcode_dist_1 2" /> |
| 213 <has_text text="--barcode_dist_2 2" /> | 216 <has_text text="--barcode_dist_2 2" /> |
| 217 <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" /> | |
| 218 <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" /> | |
| 214 <has_text text="--adapter_mm 2" /> | 219 <has_text text="--adapter_mm 2" /> |
| 215 </assert_command> | 220 </assert_command> |
| 216 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> | 221 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> |
| 217 <element name="PopA_01"> | 222 <element name="PopA_01"> |
| 218 <element name="forward" file="demultiplexed/PopA_01.1.fa" ftype="fasta"/> | 223 <element name="forward" file="demultiplexed/PopA_01.1.fa" ftype="fasta"/> |