Mercurial > repos > bimib > marea
comparison Marea/marea.xml @ 63:b8cbc2122d55 draft
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author | bimib |
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date | Mon, 16 Mar 2020 07:45:59 -0400 |
parents | ce8534417470 |
children | 858500ec9767 |
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62:ce8534417470 | 63:b8cbc2122d55 |
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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?" /> |