Mercurial > repos > bimib > marea
diff Marea/marea.xml @ 66:858500ec9767 draft
Uploaded
| author | bimib |
|---|---|
| date | Mon, 16 Mar 2020 08:25:13 -0400 |
| parents | b8cbc2122d55 |
| children | 3dfffeac4e57 |
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--- a/Marea/marea.xml Mon Mar 16 08:21:29 2020 -0400 +++ b/Marea/marea.xml Mon Mar 16 08:25:13 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.8"> +<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.1.5"> <macros> <import>marea_macros.xml</import> </macros> @@ -28,12 +28,15 @@ ${data.input_name} #end for --comparison ${cond.comparis.comparison} - #if $cond.advanced.cond_map == 'true': - --custom_rules true - --custom_rule ${cond.advanced.cond_map.custom_rule} - --custom_map ${cond.advanced.cond_map.custom_map} + #if $cond.comparis.comparison == 'onevsmany' + --control '${cond.comparis.controlgroup}' #end if + #if $cond.advanced.choice == 'true': + #if $cond.advanced.cond_map.cond_map_choice == 'true': + --custom_rules true + --custom_map ${cond.advanced.cond_map.custom_map} + #end if --pValue ${cond.advanced.pValue} --fChange ${cond.advanced.fChange} --generate_svg ${cond.advanced.generateSvg} @@ -50,14 +53,13 @@ --input_class ${input_class} --comparison ${cond.comparis.comparison} #if $cond.comparis.comparison == 'onevsmany' - --control ${cond.comparis.controlgroup} - #end if - #if $cond.advanced.cond_map == 'true': - --custom_rules true - --custom_rule ${cond.advanced.cond_map.custom_rule} - --custom_map ${cond.advanced.cond_map.custom_map} + --control '${cond.comparis.controlgroup}' #end if #if $cond.advanced.choice == 'true': + #if $cond.advanced.cond_map.cond_map_choice == 'true': + --custom_rules true + --custom_map ${cond.advanced.cond_map.custom_map} + #end if --pValue ${cond.advanced.pValue} --fChange ${cond.advanced.fChange} --generate_svg ${cond.advanced.generateSvg} @@ -100,12 +102,11 @@ <when value="false"></when> <when value="true"> <conditional name="cond_map"> - <param name="choice" type="boolean" checked="false" label="Use custom map and rules?" help="Use this option only if you have generated RAS using a custom set of rules"> + <param name="cond_map_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"> <option value="false" selected="true">No</option> <option value="true">Yes</option> </param> - <when value="true"> - <param name="Custom_rule" argument="--custom_rule" type="data" format="tabular, csv, tsv, xml" label="Custom rules" /> + <when value="true"> <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> </when> </conditional> @@ -137,13 +138,12 @@ <when value="false"></when> <when value="true"> <conditional name="cond_map"> - <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"> + <param name="cond_map_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"> <option value="false" selected="true">No</option> <option value="true">Yes</option> </param> - <when value="true"> - <param name="Custom_rule" argument="--custom_rule" type="data" format="tabular, csv, tsv, xml" label="Custom rules" /> - <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> + <when value="true"> + <param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> </when> </conditional> <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />