Mercurial > repos > iuc > stacks_procrad
comparison stacks_procrad.xml @ 6:2837e6ae4e18 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78
| author | iuc |
|---|---|
| date | Thu, 06 Apr 2017 18:17:36 -0400 |
| parents | c2733bcc51f7 |
| children | bec1f08cdfcc |
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| 5:f7bb36b55a20 | 6:2837e6ae4e18 |
|---|---|
| 58 | 58 |
| 59 -y $outype | 59 -y $outype |
| 60 | 60 |
| 61 $capture | 61 $capture |
| 62 | 62 |
| 63 $options_advanced.retain_header | |
| 64 | |
| 63 #if str($options_advanced.truncate): | 65 #if str($options_advanced.truncate): |
| 64 -t $options_advanced.truncate | 66 -t $options_advanced.truncate |
| 65 #end if | 67 #end if |
| 66 | 68 |
| 67 -w $options_advanced.sliding | 69 -w $options_advanced.sliding |
| 134 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" /> | 136 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" /> |
| 135 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/> | 137 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/> |
| 136 <param name="score" type="integer" value="10" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10)" /> | 138 <param name="score" type="integer" value="10" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10)" /> |
| 137 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/> | 139 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/> |
| 138 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" /> | 140 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" /> |
| 141 <param name="retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" /> | |
| 139 </section> | 142 </section> |
| 140 | 143 |
| 141 <!-- Stacks can produce fastq.gz and fasta.gz output but we don't propose it as they are not very common datatypes in galaxy --> | 144 <!-- Stacks can produce fastq.gz and fasta.gz output but we don't propose it as they are not very common datatypes in galaxy --> |
| 142 <param name="outype" argument="-y" type="select" label="Output format" help="output type, either 'fastq' or 'fasta'" > | 145 <param name="outype" argument="-y" type="select" label="Output format" help="output type, either 'fastq' or 'fasta'" > |
| 143 <option value="fastq" selected="True">fastq</option> | 146 <option value="fastq" selected="True">fastq</option> |
| 216 <param name="barcode" value="procrad/barcodes"/> | 219 <param name="barcode" value="procrad/barcodes"/> |
| 217 <param name="options_enzyme_selector" value="1"/> | 220 <param name="options_enzyme_selector" value="1"/> |
| 218 <param name="enzyme" value="ecoRI"/> | 221 <param name="enzyme" value="ecoRI"/> |
| 219 <param name="discard" value="true"/> | 222 <param name="discard" value="true"/> |
| 220 <param name="capture" value="true"/> | 223 <param name="capture" value="true"/> |
| 224 <param name="retain_header" value="true"/> | |
| 225 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> | |
| 226 <output_collection name="demultiplexed"> | |
| 227 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fq.header"/> | |
| 228 </output_collection> | |
| 229 <output_collection name="remaining"> | |
| 230 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fq"/> | |
| 231 </output_collection> | |
| 232 <output_collection name="discarded"> | |
| 233 <element name="R1"> | |
| 234 <assert_contents> | |
| 235 <has_text text="lane1_fakedata0_11" /> | |
| 236 </assert_contents> | |
| 237 </element> | |
| 238 </output_collection> | |
| 239 </test> | |
| 240 <test> | |
| 241 <param name="options_type_selector" value="paired"/> | |
| 242 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/> | |
| 243 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/> | |
| 244 <param name="barcode" value="procrad/barcodes"/> | |
| 245 <param name="options_enzyme_selector" value="1"/> | |
| 246 <param name="enzyme" value="ecoRI"/> | |
| 247 <param name="discard" value="true"/> | |
| 248 <param name="capture" value="true"/> | |
| 221 <param name="outype" value="fasta"/> | 249 <param name="outype" value="fasta"/> |
| 222 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> | 250 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> |
| 223 <output_collection name="demultiplexed"> | 251 <output_collection name="demultiplexed"> |
| 224 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fa"/> | 252 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fa"/> |
| 225 </output_collection> | 253 </output_collection> |