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comparison Marea/marea.xml @ 66:858500ec9767 draft

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author bimib
date Mon, 16 Mar 2020 08:25:13 -0400
parents b8cbc2122d55
children 3dfffeac4e57
comparison
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65:a61733753aec 66:858500ec9767
1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.8"> 1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.1.5">
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 $cond.comparis.comparison == 'onevsmany'
32 --custom_rules true 32 --control '${cond.comparis.controlgroup}'
33 --custom_rule ${cond.advanced.cond_map.custom_rule}
34 --custom_map ${cond.advanced.cond_map.custom_map}
35 #end if 33 #end if
34
36 #if $cond.advanced.choice == 'true': 35 #if $cond.advanced.choice == 'true':
36 #if $cond.advanced.cond_map.cond_map_choice == 'true':
37 --custom_rules true
38 --custom_map ${cond.advanced.cond_map.custom_map}
39 #end if
37 --pValue ${cond.advanced.pValue} 40 --pValue ${cond.advanced.pValue}
38 --fChange ${cond.advanced.fChange} 41 --fChange ${cond.advanced.fChange}
39 --generate_svg ${cond.advanced.generateSvg} 42 --generate_svg ${cond.advanced.generateSvg}
40 --generate_pdf ${cond.advanced.generatePdf} 43 --generate_pdf ${cond.advanced.generatePdf}
41 #else 44 #else
48 #elif $cond.type_selector == 'dataset_class': 51 #elif $cond.type_selector == 'dataset_class':
49 --input_data ${input_data} 52 --input_data ${input_data}
50 --input_class ${input_class} 53 --input_class ${input_class}
51 --comparison ${cond.comparis.comparison} 54 --comparison ${cond.comparis.comparison}
52 #if $cond.comparis.comparison == 'onevsmany' 55 #if $cond.comparis.comparison == 'onevsmany'
53 --control ${cond.comparis.controlgroup} 56 --control '${cond.comparis.controlgroup}'
54 #end if
55 #if $cond.advanced.cond_map == 'true':
56 --custom_rules true
57 --custom_rule ${cond.advanced.cond_map.custom_rule}
58 --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':
59 #if $cond.advanced.cond_map.cond_map_choice == 'true':
60 --custom_rules true
61 --custom_map ${cond.advanced.cond_map.custom_map}
62 #end if
61 --pValue ${cond.advanced.pValue} 63 --pValue ${cond.advanced.pValue}
62 --fChange ${cond.advanced.fChange} 64 --fChange ${cond.advanced.fChange}
63 --generate_svg ${cond.advanced.generateSvg} 65 --generate_svg ${cond.advanced.generateSvg}
64 --generate_pdf ${cond.advanced.generatePdf} 66 --generate_pdf ${cond.advanced.generatePdf}
65 #else 67 #else
98 <option value="false">Yes</option> 100 <option value="false">Yes</option>
99 </param> 101 </param>
100 <when value="false"></when> 102 <when value="false"></when>
101 <when value="true"> 103 <when value="true">
102 <conditional name="cond_map"> 104 <conditional name="cond_map">
103 <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"> 105 <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">
104 <option value="false" selected="true">No</option> 106 <option value="false" selected="true">No</option>
105 <option value="true">Yes</option> 107 <option value="true">Yes</option>
106 </param> 108 </param>
107 <when value="true"> 109 <when value="true">
108 <param name="Custom_rule" argument="--custom_rule" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
109 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> 110 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
110 </when> 111 </when>
111 </conditional> 112 </conditional>
112 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" /> 113 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
113 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> 114 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
135 <option value="false">Yes</option> 136 <option value="false">Yes</option>
136 </param> 137 </param>
137 <when value="false"></when> 138 <when value="false"></when>
138 <when value="true"> 139 <when value="true">
139 <conditional name="cond_map"> 140 <conditional name="cond_map">
140 <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"> 141 <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">
141 <option value="false" selected="true">No</option> 142 <option value="false" selected="true">No</option>
142 <option value="true">Yes</option> 143 <option value="true">Yes</option>
143 </param> 144 </param>
144 <when value="true"> 145 <when value="true">
145 <param name="Custom_rule" argument="--custom_rule" type="data" format="tabular, csv, tsv, xml" label="Custom rules" /> 146 <param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
146 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
147 </when> 147 </when>
148 </conditional> 148 </conditional>
149 <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="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
150 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> 150 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
151 <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" /> 151 <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" />