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comparison Marea/marea.xml @ 63:b8cbc2122d55 draft

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author bimib
date Mon, 16 Mar 2020 07:45:59 -0400
parents ce8534417470
children 858500ec9767
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62:ce8534417470 63:b8cbc2122d55
1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.1.4"> 1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.8">
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 31 #if $cond.advanced.cond_map == 'true':
32 --custom_rules true
33 --custom_rule ${cond.advanced.cond_map.custom_rule}
34 --custom_map ${cond.advanced.cond_map.custom_map}
35 #end if
32 #if $cond.advanced.choice == 'true': 36 #if $cond.advanced.choice == 'true':
33 #if $cond.advanced.cond_map.cond_map_choice == 'true':
34 --custom_rules true
35 --custom_map ${cond.advanced.cond_map.custom_map}
36 #end if
37 --pValue ${cond.advanced.pValue} 37 --pValue ${cond.advanced.pValue}
38 --fChange ${cond.advanced.fChange} 38 --fChange ${cond.advanced.fChange}
39 --generate_svg ${cond.advanced.generateSvg} 39 --generate_svg ${cond.advanced.generateSvg}
40 --generate_pdf ${cond.advanced.generatePdf} 40 --generate_pdf ${cond.advanced.generatePdf}
41 #else 41 #else
50 --input_class ${input_class} 50 --input_class ${input_class}
51 --comparison ${cond.comparis.comparison} 51 --comparison ${cond.comparis.comparison}
52 #if $cond.comparis.comparison == 'onevsmany' 52 #if $cond.comparis.comparison == 'onevsmany'
53 --control ${cond.comparis.controlgroup} 53 --control ${cond.comparis.controlgroup}
54 #end if 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
55 #if $cond.advanced.choice == 'true': 60 #if $cond.advanced.choice == 'true':
56 #if $cond.advanced.cond_map.cond_map_choice == 'true':
57 --custom_rules true
58 --custom_map ${cond.advanced.cond_map.custom_map}
59 #end if
60 --pValue ${cond.advanced.pValue} 61 --pValue ${cond.advanced.pValue}
61 --fChange ${cond.advanced.fChange} 62 --fChange ${cond.advanced.fChange}
62 --generate_svg ${cond.advanced.generateSvg} 63 --generate_svg ${cond.advanced.generateSvg}
63 --generate_pdf ${cond.advanced.generatePdf} 64 --generate_pdf ${cond.advanced.generatePdf}
64 #else 65 #else
97 <option value="false">Yes</option> 98 <option value="false">Yes</option>
98 </param> 99 </param>
99 <when value="false"></when> 100 <when value="false"></when>
100 <when value="true"> 101 <when value="true">
101 <conditional name="cond_map"> 102 <conditional name="cond_map">
102 <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"> 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">
103 <option value="false" selected="true">No</option> 104 <option value="false" selected="true">No</option>
104 <option value="true">Yes</option> 105 <option value="true">Yes</option>
105 </param> 106 </param>
106 <when value="true"> 107 <when value="true">
108 <param name="Custom_rule" argument="--custom_rule" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
107 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> 109 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
108 </when> 110 </when>
109 </conditional> 111 </conditional>
110 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" /> 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" />
111 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> 113 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
133 <option value="false">Yes</option> 135 <option value="false">Yes</option>
134 </param> 136 </param>
135 <when value="false"></when> 137 <when value="false"></when>
136 <when value="true"> 138 <when value="true">
137 <conditional name="cond_map"> 139 <conditional name="cond_map">
138 <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"> 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">
139 <option value="false" selected="true">No</option> 141 <option value="false" selected="true">No</option>
140 <option value="true">Yes</option> 142 <option value="true">Yes</option>
141 </param> 143 </param>
142 <when value="true"> 144 <when value="true">
143 <param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> 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"/>
144 </when> 147 </when>
145 </conditional> 148 </conditional>
146 <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" />
147 <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" />
148 <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?" />