Mercurial > repos > ecology > pampa_glmcomm

comparison PAMPA_GLM.xml @ 4:44b9069775ca draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
author ecology
date Sun, 22 Nov 2020 18:40:23 +0000
parents 97967fbcf6da
children 8db02073b671
comparison
equal deleted inserted replaced
3:97967fbcf6da 4:44b9069775ca
13 '$varrep' 13 '$varrep'
14 '$varrand' 14 '$varrand'
15 '$sep' 15 '$sep'
16 #if $settings.advanced=='advanced' 16 #if $settings.advanced=='advanced'
17 $settings.distrib 17 $settings.distrib
18 'FALSE' 18 $settings.rdata
19 #else 19 #else
20 'None' 20 'None'
21 'FALSE' 21 'false'
22 #end if 22 #end if
23 'unit' 23 'unit'
24 '$__tool_directory__/FunctPAMPAGalaxy.r' 24 '$__tool_directory__/FunctPAMPAGalaxy.r'
25 '$output_summary' 25 '$output_summary'
26 '$output_recap' 26 '$output_recap'
27 '$output_rate'
28 #if $settings.advanced=='advanced'
29 #if $settings.rdata=='true'
30 '$output_GLM'
31 #end if
32 #end if
27 ]]> 33 ]]>
28 </command> 34 </command>
29 <inputs> 35 <inputs>
30 <expand macro="pampa_input_GLM"/> 36 <expand macro="pampa_input_GLM"/>
31 <param name="sep" type="data_column" data_ref="input_unitobs" force_select="false" label="Separation factor of your analysis from unitobs file" help= "Choose the field of the separation factor, for each level of this factor, one GLM will be computed."/> 37 <param name="sep" type="data_column" data_ref="input_unitobs" force_select="false" label="Separation factor of your analysis from unitobs file" help= "Choose the field of the separation factor, for each level of this factor, one GLM will be computed."/>
37 <outputs> 43 <outputs>
38 <data name="output_summary" from_work_dir="GLMSummary.tabular" format="tabular" label="GLM - Results from your community analysis on ${on_string}"/> 44 <data name="output_summary" from_work_dir="GLMSummary.tabular" format="tabular" label="GLM - Results from your community analysis on ${on_string}"/>
39 <expand macro="pampa_output_GLM"/> 45 <expand macro="pampa_output_GLM"/>
40 </outputs> 46 </outputs>
41 <tests> 47 <tests>
42 <test> 48 <test expect_num_outputs="4">
43 <param name="input_metric" value="Community_metrics_cropped.tabular"/> 49 <param name="input_metric" value="Community_metrics_cropped.tabular"/>
44 <param name="input_unitobs" value="Unitobs.tabular"/> 50 <param name="input_unitobs" value="Unitobs.tabular"/>
45 <param name="varint" value="4"/> 51 <param name="varint" value="4"/>
46 <param name="varrep" value="year,site,habitat"/> 52 <param name="varrep" value="year,site,habitat"/>
47 <param name="varrand" value="site"/> 53 <param name="varrand" value="site"/>
48 <param name="sep" value="22"/> 54 <param name="sep" value="22"/>
49 <param name="advanced" value="simple"/> 55 <param name="advanced" value="advanced"/>
56 <param name="distrib" value="None"/>
57 <param name="rdata" value="true"/>
50 <output name="output_summary"> 58 <output name="output_summary">
51 <assert_contents> 59 <assert_contents>
52 <has_n_lines n="9"/> 60 <has_n_lines n="9"/>
53 </assert_contents> 61 </assert_contents>
54 </output> 62 </output>
55 <output name="output_recap"> 63 <output name="output_recap">
56 <assert_contents> 64 <assert_contents>
57 <has_n_lines n="413"/> 65 <has_n_lines n="412"/>
58 </assert_contents> 66 </assert_contents>
59 </output> 67 </output>
60 <output name="output_rate"> 68 <output name="output_rate">
61 <assert_contents> 69 <assert_contents>
62 <has_n_lines n="51"/> 70 <has_n_lines n="50"/>
63 </assert_contents> 71 </assert_contents>
64 </output> 72 </output>
73 <output_collection name="output_GLM" type="list" count="3">
74 <element name="GLM_HR" ftype="Rdata">
75 <assert_contents>
76 <has_size value="185018" delta="10000"/>
77 </assert_contents>
78 </element>
79 <element name="GLM_RE" ftype="Rdata">
80 <assert_contents>
81 <has_size value="168685" delta="10000"/>
82 </assert_contents>
83 </element>
84 <element name="global_GLM" ftype="Rdata">
85 <assert_contents>
86 <has_size value="195910" delta="10000"/>
87 </assert_contents>
88 </element>
89 </output_collection>
65 </test> 90 </test>
66 </tests> 91 </tests>
67 <edam_topics> 92 <edam_topics>
68 <edam_topic>topic_0610</edam_topic> 93 <edam_topic>topic_0610</edam_topic>
69 <edam_topic>topic_3050</edam_topic> 94 <edam_topic>topic_3050</edam_topic>
116 The first input may be extracted from the 'Calculate community metrics' tool. 141 The first input may be extracted from the 'Calculate community metrics' tool.
117 142
118 A tabular file with unitobs or location data which contains at least as much columns as used response variables and separation factor in addition with the 'observation.unit' or 'location' column. 143 A tabular file with unitobs or location data which contains at least as much columns as used response variables and separation factor in addition with the 'observation.unit' or 'location' column.
119 144
120 +--------------------------------+---------+--------+------------+-----+ 145 +--------------------------------+---------+--------+------------+-----+
121 | observation.unit OR location | ??site? | year | habitat | ... | 146 | observation.unit OR location | site | year | habitat | ... |
122 +================================+=========+========+============+=====+ 147 +================================+=========+========+============+=====+
123 | site_yearID OR locationID | site ID | 2000 | habitatID | ... | 148 | site_yearID OR locationID | site ID | 2000 | habitatID | ... |
124 +--------------------------------+---------+--------+------------+-----+ 149 +--------------------------------+---------+--------+------------+-----+
125 | ... | ... | ... | ... | ... | 150 | ... | ... | ... | ... | ... |
126 +--------------------------------+---------+--------+------------+-----+ 151 +--------------------------------+---------+--------+------------+-----+
152
153 The site may represent the same entity as the location or represent an aggregation of several locations
127 154
128 | 155 |
129 156
130 **Output** 157 **Output**
131 158
140 **Source** 167 **Source**
141 168
142 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht. 169 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
143 170
144 ]]></help> 171 ]]></help>
145
146 <expand macro="pampa_bibref" /> 172 <expand macro="pampa_bibref" />
147 </tool> 173 </tool>