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comparison PAMPA_GLM_SP.xml @ 2:6c14021f678e draft

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
author ecology
date Sun, 22 Nov 2020 18:40:40 +0000
parents e972fe2bffee
children c12897ba5f83
comparison
equal deleted inserted replaced
1:e972fe2bffee 2:6c14021f678e
13 '$varrep' 13 '$varrep'
14 '$varrand' 14 '$varrand'
15 'species.code' 15 'species.code'
16 #if $settings.advanced=='advanced' 16 #if $settings.advanced=='advanced'
17 $settings.distrib 17 $settings.distrib
18 'FALSE' 18 $settings.rdata
19 #else 19 #else
20 'None' 20 'None'
21 'FALSE' 21 'false'
22 #end if 22 #end if
23 'unitSp' 23 'unitSp'
24 '$__tool_directory__/FunctPAMPAGalaxy.r' 24 '$__tool_directory__/FunctPAMPAGalaxy.r'
25 '$output_summary' 25 '$output_summary'
26 '$output_recap' 26 '$output_recap'
27 #if $settings.advanced=='advanced'
28 #if $settings.rdata=='true'
29 '$output_GLM'
30 #end if
31 #end if
27 ]]> 32 ]]>
28 </command> 33 </command>
29 <inputs> 34 <inputs>
30 <expand macro="pampa_input_GLM"/> 35 <expand macro="pampa_input_GLM"/>
31 <expand macro="pampa_var_GLM"/> 36 <expand macro="pampa_var_GLM"/>
32 <conditional name="settings"> 37 <conditional name="settings">
33 <expand macro="pampa_advanced_params_select_GLM"/> 38 <expand macro="pampa_advanced_params_select_GLM"/>
34 </conditional> 39 </conditional>
35 </inputs> 40 </inputs>
36 <outputs> 41 <outputs>
37
38 <data name="output_summary" from_work_dir="GLMSummary.tabular" format="tabular" label="GLM - Results from your population analysis on ${on_string}"/> 42 <data name="output_summary" from_work_dir="GLMSummary.tabular" format="tabular" label="GLM - Results from your population analysis on ${on_string}"/>
39 <expand macro="pampa_output_GLM"/> 43 <expand macro="pampa_output_GLM"/>
40 </outputs> 44 </outputs>
41 <tests> 45 <tests>
42 <test> 46 <test expect_num_outputs="4">
43 <param name="input_metric" value="Presence_absence_table_sansszcl_cropped.tabular"/> 47 <param name="input_metric" value="Presence_absence_table_sansszcl_cropped.tabular"/>
44 <param name="input_unitobs" value="Unitobs.tabular"/> 48 <param name="input_unitobs" value="Unitobs.tabular"/>
45 <param name="varint" value="4"/> 49 <param name="varint" value="4"/>
46 <param name="varrep" value="year,site,habitat"/> 50 <param name="varrep" value="year,site,habitat"/>
47 <param name="varrand" value="site"/> 51 <param name="varrand" value="site"/>
48 <param name="advanced" value="simple"/> 52 <param name="advanced" value="advanced"/>
53 <param name="distrib" value="None"/>
54 <param name="rdata" value="true"/>
49 <output name="output_summary"> 55 <output name="output_summary">
50 <assert_contents> 56 <assert_contents>
51 <has_n_lines n="4"/> 57 <has_n_lines n="4"/>
52 </assert_contents> 58 </assert_contents>
53 </output> 59 </output>
54 <output name="output_recap"> 60 <output name="output_recap">
55 <assert_contents> 61 <assert_contents>
56 <has_n_lines n="607"/> 62 <has_n_lines n="606"/>
57 </assert_contents> 63 </assert_contents>
58 </output> 64 </output>
59 <output name="output_rate"> 65 <output name="output_rate">
60 <assert_contents> 66 <assert_contents>
61 <has_n_lines n="46"/> 67 <has_n_lines n="45"/>
62 </assert_contents> 68 </assert_contents>
63 </output> 69 </output>
70 <output_collection name="output_GLM" type="list" count="3">
71 <element name="GLM_Abalstel" ftype="Rdata">
72 <assert_contents>
73 <has_size value="199219" delta="10000"/>
74 </assert_contents>
75 </element>
76 <element name="GLM_Hemifasc" ftype="Rdata">
77 <assert_contents>
78 <has_size value="202264" delta="10000"/>
79 </assert_contents>
80 </element>
81 <element name="GLM_Zebrscop" ftype="Rdata">
82 <assert_contents>
83 <has_size value="207311" delta="10000"/>
84 </assert_contents>
85 </element>
86 </output_collection>
64 </test> 87 </test>
65 </tests> 88 </tests>
66 <edam_topics> 89 <edam_topics>
67 <edam_topic>topic_0610</edam_topic> 90 <edam_topic>topic_0610</edam_topic>
68 <edam_topic>topic_3050</edam_topic> 91 <edam_topic>topic_3050</edam_topic>
124 | site_yearID OR locationID | species code | site ID | 2000 | habitatID | ... | 147 | site_yearID OR locationID | species code | site ID | 2000 | habitatID | ... |
125 +--------------------------------+--------------+---------+--------+------------+-----+ 148 +--------------------------------+--------------+---------+--------+------------+-----+
126 | ... | ... | ... | ... | ... | ... | 149 | ... | ... | ... | ... | ... | ... |
127 +--------------------------------+--------------+---------+--------+------------+-----+ 150 +--------------------------------+--------------+---------+--------+------------+-----+
128 151
152 The site may represent the same entity as the location or represent an aggregation of several locations.
153
129 | 154 |
130 155
131 **Output** 156 **Output**
132 157
133 Two text files : 158 Two text files :