Mercurial > repos > thanhlv > nullarbor
comparison nullarbor.xml @ 3:63ba2e9353bb draft default tip
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
| author | thanhlv |
|---|---|
| date | Mon, 06 May 2019 08:05:32 -0400 |
| parents | 4c3fb37e628d |
| children |
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| 2:4c3fb37e628d | 3:63ba2e9353bb |
|---|---|
| 9 <expand macro="env" /> | 9 <expand macro="env" /> |
| 10 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
| 11 | 11 |
| 12 nullarbor.pl | 12 nullarbor.pl |
| 13 --run | 13 --run |
| 14 --cpus $opt.cpus | 14 --cpus '$opt.cpus' |
| 15 | 15 |
| 16 #if $opt.verbose | 16 #if '$opt.verbose' |
| 17 $opt.verbose | 17 '$opt.verbose' |
| 18 #end if | 18 #end if |
| 19 | 19 |
| 20 --gcode $adv_opt.gcode | 20 --gcode $adv_opt.gcode |
| 21 | 21 |
| 22 #if $adv_opt.trim | 22 #if $adv_opt.trim |
| 39 --mask $adv_opt.mask | 39 --mask $adv_opt.mask |
| 40 #end if | 40 #end if |
| 41 | 41 |
| 42 --assembler $plugins.assembler | 42 --assembler $plugins.assembler |
| 43 | 43 |
| 44 #if str($plugins.assembler-opt) != "" | 44 #if str($plugins.assembler_opt) != "" |
| 45 --assembler-opt $plugins.assembler-opt | 45 --assembler_opt $plugins.assembler_opt |
| 46 #end if | 46 #end if |
| 47 | 47 |
| 48 --treebuilder $plugins.treebuilder | 48 --treebuilder $plugins.treebuilder |
| 49 | 49 |
| 50 #if str($plugins.treebuilder-opt) != "" | 50 #if str($plugins.treebuilder_opt) != "" |
| 51 --treebuilder-opt $plugins.treebuilder-opt | 51 --treebuilder_opt $plugins.treebuilder_opt |
| 52 #end if | 52 #end if |
| 53 | 53 |
| 54 --taxoner $plugins.taxoner | 54 --taxoner $plugins.taxoner |
| 55 | 55 |
| 56 #if str($plugins.taxoner-opt) != "" | 56 #if str($plugins.taxoner_opt) != "" |
| 57 --taxoner-opt $plugins.taxoner-opt | 57 --taxoner_opt $plugins.taxoner_opt |
| 58 #end if | 58 #end if |
| 59 | 59 |
| 60 --annotator $plugins.annotator | 60 --annotator $plugins.annotator |
| 61 | 61 |
| 62 #if str($plugins.annotator-opt) != "" | 62 #if str($plugins.annotator_opt) != "" |
| 63 --annotator-opt $plugins.annotator-opt | 63 --annotator_opt $plugins.annotator_opt |
| 64 #end if | 64 #end if |
| 65 | 65 |
| 66 --name $name | 66 --name $name |
| 67 --ref $ref | 67 --ref $ref |
| 68 --input $tab_file | 68 --input $tab_file |
| 73 <inputs> | 73 <inputs> |
| 74 <param name="tab_file" format="txt" type="data" label="Tab file generated from nullarbor_prepare" help="You need to run nullarbor_test for generating a tab file of reads before running this tool"/> | 74 <param name="tab_file" format="txt" type="data" label="Tab file generated from nullarbor_prepare" help="You need to run nullarbor_test for generating a tab file of reads before running this tool"/> |
| 75 <param name="ref" type="data" format="fasta" label="Reference genome " help="Reference file in FASTA or GBK format"/> | 75 <param name="ref" type="data" format="fasta" label="Reference genome " help="Reference file in FASTA or GBK format"/> |
| 76 <param name="name" type="text" optional="False" label="Job name" help="" /> | 76 <param name="name" type="text" optional="False" label="Job name" help="" /> |
| 77 | 77 |
| 78 <section name='opt' title = "Options"> | 78 <section name="opt" title="Options"> |
| 79 <param name="cpus" argument="--cpus" type="integer" value="8" label="CPUs" help="Maximum number of CPUs to use in total (Default: 8)" /> | 79 <param name="cpus" argument="--cpus" type="integer" value="8" label="CPUs" help="Maximum number of CPUs to use in total (Default: 8)" /> |
| 80 <param name="verbose" argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose" help="More screen output" /> | 80 <param name="verbose" argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose" help="More screen output" /> |
| 81 </section> | 81 </section> |
| 82 | 82 |
| 83 <section name="adv_opt" title="Advanced Options"> | 83 <section name="adv_opt" title="Advanced Options"> |
| 84 <param name="gcode" argument="--gcode" type="integer" value="11" label="Genetic code for prokka" help="(Default: 11)" /> | 84 <param name="gcode" argument="--gcode" type="integer" value="11" label="Genetic code for prokka" help="(Default: 11)" /> |
| 85 <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" checked="False" label="Trim reads of adaptors" help="(Default: NO)" /> | 85 <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" checked="False" label="Trim reads of adaptors" help="(Default: NO)" /> |
| 230 <option value="skesa_fast">skesa fast</option> | 230 <option value="skesa_fast">skesa fast</option> |
| 231 <option value="megahit">megahit</option> | 231 <option value="megahit">megahit</option> |
| 232 <option value="shovill">shovill</option> | 232 <option value="shovill">shovill</option> |
| 233 <option value="spades">Spades</option> | 233 <option value="spades">Spades</option> |
| 234 </param> | 234 </param> |
| 235 <param name="assembler-opt" argument="--assembler-opt" type="text" value="" label="Extra assembler options to pass" help="" /> | 235 <param name="assembler_opt" argument="--assembler_opt" type="text" value="" label="Extra assembler options to pass" help="" /> |
| 236 <param name="treebuilder" argument="--treebuilder" type="select" label="Tree-builder to use" help="Which tree builder would you like to use, default is iqtree_fast"> | 236 <param name="treebuilder" argument="--treebuilder" type="select" label="Tree-builder to use" help="Which tree builder would you like to use, default is iqtree_fast"> |
| 237 <option value="fasttree">fasttree</option> | 237 <option value="fasttree">fasttree</option> |
| 238 <option value="iqtree">iqtree</option> | 238 <option value="iqtree">iqtree</option> |
| 239 <option value="iqtree_fast" selected="True">iqtree_fast</option> | 239 <option value="iqtree_fast" selected="True">iqtree_fast</option> |
| 240 <option value="iqtree_slow">iqtree_slow</option> | 240 <option value="iqtree_slow">iqtree_slow</option> |
| 241 </param> | 241 </param> |
| 242 <param name="treebuilder-opt" argument="--treebuilder-opt" type="text" value="" label="Extra tree-builder options to pass" help="" /> | 242 <param name="treebuilder_opt" argument="--treebuilder_opt" type="text" value="" label="Extra tree-builder options to pass" help="" /> |
| 243 <param name="taxoner" argument="--taxoner" type="select" label="Species ID tool to use" help="Which taxoner would you like to use, default is kraken"> | 243 <param name="taxoner" argument="--taxoner" type="select" label="Species ID tool to use" help="Which taxoner would you like to use, default is kraken"> |
| 244 <option value="kraken" selected="True">kraken</option> | 244 <option value="kraken" selected="True">kraken</option> |
| 245 <option value="centrifuge">centrifuge</option> | 245 <option value="centrifuge">centrifuge</option> |
| 246 </param> | 246 </param> |
| 247 <param name="taxoner-opt" argument="--taxoner-opt" type="text" value="" label="Extra taxoner options to pass" help="" /> | 247 <param name="taxoner_opt" argument="--taxoner_opt" type="text" value="" label="Extra taxoner options to pass" help="" /> |
| 248 <param name="annotator" argument="--annotator" type="select" label="Genome annotator to use" help="Which genome annotator would you like to use, default is prokka_fast"> | 248 <param name="annotator" argument="--annotator" type="select" label="Genome annotator to use" help="Which genome annotator would you like to use, default is prokka_fast"> |
| 249 <option value="prokka_fast" selected="True">prokka_fast</option> | 249 <option value="prokka_fast" selected="True">prokka_fast</option> |
| 250 </param> | 250 </param> |
| 251 <param name="annotator-opt" argument="--annotator-opt" type="text" value="" label="Extra annotator options to pass" help="" /> | 251 <param name="annotator_opt" argument="--annotator_opt" type="text" value="" label="Extra annotator options to pass" help="" /> |
| 252 </section> | 252 </section> |
| 253 | 253 |
| 254 </inputs> | 254 </inputs> |
| 255 | 255 |
| 256 <outputs> | 256 <outputs> |