Mercurial > repos > matnguyen > pathogist
comparison galaxy/tools/config_builder/config_builder.xml @ 3:56f1b7f06222 draft
Modified config builder
| author | matnguyen |
|---|---|
| date | Tue, 05 Mar 2019 03:41:14 -0500 |
| parents | baf1e89b42eb |
| children | 727c0e52e64e |
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| 2:baf1e89b42eb | 3:56f1b7f06222 |
|---|---|
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.2.3">pathogist</requirement> | 4 <requirement type="package" version="0.2.3">pathogist</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 | 6 |
| 7 <command><![CDATA[ | 7 <command><![CDATA[ |
| 8 PATHOGIST all config.yaml --new_config | 8 PATHOGIST all blank_config.yaml --new_config |
| 9 | 9 |
| 10 $__tool_directory__/config_builder | 10 $__tool_directory__/config_builder |
| 11 | 11 |
| 12 #if snippy.snippy_checkbox | 12 #if snippy.snippy_checkbox |
| 13 --snippy | 13 --snippy |
| 85 $adv_clustering.all_constraints | 85 $adv_clustering.all_constraints |
| 86 --method $adv_clustering.method | 86 --method $adv_clustering.method |
| 87 $adv_clustering.presolve | 87 $adv_clustering.presolve |
| 88 $adv_clustering.visualize | 88 $adv_clustering.visualize |
| 89 #endif | 89 #endif |
| 90 | |
| 91 blank_onfig.yaml | |
| 92 $forward | |
| 93 $reverse | |
| 94 config.yaml | |
| 90 ]]></command> | 95 ]]></command> |
| 91 | 96 |
| 92 | 97 |
| 93 <inputs> | 98 <inputs> |
| 94 <!--<conditional name="task">--> | 99 <param name="forward" type="data" format="txt,tabular" label="List of forward reads"/> |
| 95 <!--<param name="task_selector" type="select" label="Create Blank Config or Populate Config File">--> | 100 <param name="reverse" type="data" format="txt,tabular" label="List of reverse reads"/> |
| 96 <!--<option value="create">Create Blank Config File</option>--> | 101 |
| 97 <!--<option value="populate">Populate Config File</option>--> | |
| 98 <!--</param>--> | |
| 99 <!--<when value="create">--> | |
| 100 | |
| 101 <!--</when>--> | |
| 102 <!--<when value="populate">--> | |
| 103 <conditional name="snippy"> | 102 <conditional name="snippy"> |
| 104 <param name="snippy_checkbox" type="boolean" label="Run Snippy"/> | 103 <param name="snippy_checkbox" type="boolean" label="Run Snippy"/> |
| 105 <when value="true"> | 104 <when value="true"> |
| 106 <param name="reference" type="data" format="fasta,fa,fasta.gz,fa.gz" label="Reference Genome"/> | 105 <param name="reference" type="data" format="fasta,fa,fasta.gz,fa.gz" label="Reference Genome"/> |
| 107 <conditional name="snippy_adv"> | 106 <conditional name="snippy_adv"> |
| 185 | 184 |
| 186 <conditional name="kwip"> | 185 <conditional name="kwip"> |
| 187 <param name="kwip_checkbox" type="boolean" label="Run kWIP"/> | 186 <param name="kwip_checkbox" type="boolean" label="Run kWIP"/> |
| 188 <when value="true"> | 187 <when value="true"> |
| 189 <conditional name="kwip_adv"> | 188 <conditional name="kwip_adv"> |
| 190 <param name="kwip_adv_checkbox" type="boolean" label="Advance kWIP Parameters"/> | 189 <param name="kwip_adv_checkbox" type="boolean" label="Advanced kWIP Parameters"/> |
| 191 <when value="true"> | 190 <when value="true"> |
| 192 <param name="N" type="integer" value="1" min="1" label="Number of tables"/> | 191 <param name="N" type="integer" value="1" min="1" label="Number of tables"/> |
| 193 <param name="x" type="float" value="1e9" min="1" label="Maximum table size"/> | 192 <param name="x" type="float" value="1e9" min="1" label="Maximum table size"/> |
| 194 <param name="ksize" type="integer" value="31" min="1" label="kmer size"/> | 193 <param name="ksize" type="integer" value="31" min="1" label="kmer size"/> |
| 195 <param name="unique_kmers" type="integer" value="0" min="0" label="Approximate number | 194 <param name="unique_kmers" type="integer" value="0" min="0" label="Approximate number |
| 223 label="Perform presolving for clustering"/> | 222 label="Perform presolving for clustering"/> |
| 224 <param name="visualize" type="boolean" checked="false" falsevalue="" truevalue="--visualize" | 223 <param name="visualize" type="boolean" checked="false" falsevalue="" truevalue="--visualize" |
| 225 label="Visualize clusters"/> | 224 label="Visualize clusters"/> |
| 226 </when> | 225 </when> |
| 227 </conditional> | 226 </conditional> |
| 228 <!--</when>--> | |
| 229 <!--</conditional>--> | |
| 230 </inputs> | 227 </inputs> |
| 231 | 228 |
| 232 <outputs> | 229 <outputs> |
| 233 <data name="output" label="PathOGiST Config File" format="yaml" from_work_dir="config.yaml"/> | 230 <data name="output" label="PathOGiST Config File" format="yaml" from_work_dir="config.yaml"/> |
| 234 </outputs> | 231 </outputs> |