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comparison Marea/marea.xml @ 57:dcb817af5d81 draft

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Uploaded
author bimib
date Sun, 15 Mar 2020 11:29:01 -0400
parents 39238e5840ae
children 959a9cb7816a
comparison
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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" />