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comparison Marea/marea.xml @ 58:959a9cb7816a draft

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Uploaded
author bimib
date Sun, 15 Mar 2020 11:37:31 -0400
parents dcb817af5d81
children d4bc7c7882c3
comparison
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57:dcb817af5d81 58:959a9cb7816a
1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.1.0"> 1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.1.1">
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>
26 --names 26 --names
27 #for $data in $cond.input_Datasets: 27 #for $data in $cond.input_Datasets:
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.cond_map_choice} == 'true':
32 --custom_rules true 32 --custom_rules true
33 --custom_map ${cond.advanced.cond_map.custom_map} 33 --custom_map ${cond.advanced.cond_map.custom_map}
34 #end if 34 #end if
35 #if $cond.advanced.choice == 'true': 35 #if $cond.advanced.choice == 'true':
36 --pValue ${cond.advanced.pValue} 36 --pValue ${cond.advanced.pValue}
49 --input_class ${input_class} 49 --input_class ${input_class}
50 --comparison ${cond.comparis.comparison} 50 --comparison ${cond.comparis.comparison}
51 #if $cond.comparis.comparison == 'onevsmany' 51 #if $cond.comparis.comparison == 'onevsmany'
52 --control ${cond.comparis.controlgroup} 52 --control ${cond.comparis.controlgroup}
53 #end if 53 #end if
54 #if $cond.advanced.cond_map == 'true': 54 #if $cond.advanced.cond_map.cond_map_choice == 'true':
55 --custom_rules true 55 --custom_rules true
56 --custom_map ${cond.advanced.cond_map.custom_map} 56 --custom_map ${cond.advanced.cond_map.custom_map}
57 #end if 57 #end if
58 #if $cond.advanced.choice == 'true': 58 #if $cond.advanced.choice == 'true':
59 --pValue ${cond.advanced.pValue} 59 --pValue ${cond.advanced.pValue}
96 <option value="false">Yes</option> 96 <option value="false">Yes</option>
97 </param> 97 </param>
98 <when value="false"></when> 98 <when value="false"></when>
99 <when value="true"> 99 <when value="true">
100 <conditional name="cond_map"> 100 <conditional name="cond_map">
101 <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"> 101 <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">
102 <option value="false" selected="true">No</option> 102 <option value="false" selected="true">No</option>
103 <option value="true">Yes</option> 103 <option value="true">Yes</option>
104 </param> 104 </param>
105 <when value="true"> 105 <when value="true">
106 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> 106 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
132 <option value="false">Yes</option> 132 <option value="false">Yes</option>
133 </param> 133 </param>
134 <when value="false"></when> 134 <when value="false"></when>
135 <when value="true"> 135 <when value="true">
136 <conditional name="cond_map"> 136 <conditional name="cond_map">
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"> 137 <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">
138 <option value="false" selected="true">No</option> 138 <option value="false" selected="true">No</option>
139 <option value="true">Yes</option> 139 <option value="true">Yes</option>
140 </param> 140 </param>
141 <when value="true"> 141 <when value="true">
142 <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"/>