Mercurial > repos > bimib > marea
comparison Marea/marea.xml @ 57:dcb817af5d81 draft
Uploaded
| author | bimib |
|---|---|
| date | Sun, 15 Mar 2020 11:29:01 -0400 |
| parents | 39238e5840ae |
| children | 959a9cb7816a |
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| 56:68375ead0ee4 | 57:dcb817af5d81 |
|---|---|
| 1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.9"> | 1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.1.0"> |
| 2 <macros> | 2 <macros> |
| 3 <import>marea_macros.xml</import> | 3 <import>marea_macros.xml</import> |
| 4 </macros> | 4 </macros> |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="package" version="0.23.0">pandas</requirement> | 6 <requirement type="package" version="0.23.0">pandas</requirement> |
| 28 ${data.input_name} | 28 ${data.input_name} |
| 29 #end for | 29 #end for |
| 30 --comparison ${cond.comparis.comparison} | 30 --comparison ${cond.comparis.comparison} |
| 31 #if $cond.advanced.cond_map == 'true': | 31 #if $cond.advanced.cond_map == 'true': |
| 32 --custom_rules true | 32 --custom_rules true |
| 33 --custom_rule ${cond.advanced.cond_map.custom_rule} | |
| 34 --custom_map ${cond.advanced.cond_map.custom_map} | 33 --custom_map ${cond.advanced.cond_map.custom_map} |
| 35 #end if | 34 #end if |
| 36 #if $cond.advanced.choice == 'true': | 35 #if $cond.advanced.choice == 'true': |
| 37 --pValue ${cond.advanced.pValue} | 36 --pValue ${cond.advanced.pValue} |
| 38 --fChange ${cond.advanced.fChange} | 37 --fChange ${cond.advanced.fChange} |
| 52 #if $cond.comparis.comparison == 'onevsmany' | 51 #if $cond.comparis.comparison == 'onevsmany' |
| 53 --control ${cond.comparis.controlgroup} | 52 --control ${cond.comparis.controlgroup} |
| 54 #end if | 53 #end if |
| 55 #if $cond.advanced.cond_map == 'true': | 54 #if $cond.advanced.cond_map == 'true': |
| 56 --custom_rules true | 55 --custom_rules true |
| 57 --custom_rule ${cond.advanced.cond_map.custom_rule} | |
| 58 --custom_map ${cond.advanced.cond_map.custom_map} | 56 --custom_map ${cond.advanced.cond_map.custom_map} |
| 59 #end if | 57 #end if |
| 60 #if $cond.advanced.choice == 'true': | 58 #if $cond.advanced.choice == 'true': |
| 61 --pValue ${cond.advanced.pValue} | 59 --pValue ${cond.advanced.pValue} |
| 62 --fChange ${cond.advanced.fChange} | 60 --fChange ${cond.advanced.fChange} |
| 138 <conditional name="cond_map"> | 136 <conditional name="cond_map"> |
| 139 <param name="choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules"> | 137 <param name="choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules"> |
| 140 <option value="false" selected="true">No</option> | 138 <option value="false" selected="true">No</option> |
| 141 <option value="true">Yes</option> | 139 <option value="true">Yes</option> |
| 142 </param> | 140 </param> |
| 143 <when value="true"> | 141 <when value="true"> |
| 144 <param name="Custom_rule" argument="--custom_rule" type="data" format="tabular, csv, tsv, xml" label="Custom rules" /> | |
| 145 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> | 142 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> |
| 146 </when> | 143 </when> |
| 147 </conditional> | 144 </conditional> |
| 148 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" /> | 145 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" /> |
| 149 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> | 146 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> |