Mercurial > repos > ecology > stoc_mainglm_group

annotate mainglm_group.xml @ 2:6cfbb72f9dab draft default tip

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"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"
author ecology
date Mon, 11 May 2020 21:15:20 +0000
parents 16179eb29175
children
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16179eb29175 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit 5d749f3befe0a1f517c8af5f757e5b332d6374a2"
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1 <tool id="stoceps_glm_group" name="Estimate temporal population variation" version="@VERSION@">
0
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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2 <description>by specialization group</description>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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3 <macros>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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4 <import>stoceps_macros.xml</import>
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5 </macros>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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6 <expand macro="mainglm_requirements"/>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript
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9 '$__tool_directory__/ExeMainglmParGroupGalaxy.r'
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10 '$input_y_var'
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11 '$input_glob_tendencies'
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12 '$inputtabSpecies'
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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13 'mainglm_group'
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14 #if $settings.advanced=='advanced'
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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15 $settings.sp_code
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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16 #else
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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17 ''
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18 #end if
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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19 '$__tool_directory__/FunctTrendSTOCGalaxy.r'
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20 '$__tool_directory__/biais.tabular'
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21
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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22 '$data_group'
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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23 '$year_var_group'
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24 '$glob_tend_group'
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25 ]]>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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26 </command>
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27 <inputs>
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28 <param name="input_y_var" type="data" format="tabular" label="Yearly variation dataset" help="Output from the 'Estimate temporal population evoution by species' tool."/>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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29 <param name="input_glob_tendencies" type="data" format="tabular" label="Global tendencies dataset" help="Output from the 'Estimate temporal population evoution by species' tool."/>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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30 <param name="inputtabSpecies" type="data" format="tabular" label="Species file" help="Input species tabular file, with 5 columns (species ID, species name, species scientific name, specialization status)." />
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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31 <conditional name="settings">
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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32 <expand macro="stoceps_advanced_params_select"/>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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33 <when value="advanced">
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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34 <param name="sp_code" type="select" label="Filter species to exclude" help="Create a subsample by selecting the species codes you don't want to use." multiple="true" optional="true">
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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35 <options from_dataset="input_glob_tendencies">
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36 <column name="value" index="1"/>
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37 <filter type="unique_value" name="espece" column="1"/>
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38 </options>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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39 <sanitizer>
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40 <valid initial="string.printable">
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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41 <remove value="&quot;"/>
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42 </valid>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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43 </sanitizer>
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44 </param>
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45 </when>
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46 </conditional>
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47 </inputs>
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48 <outputs>
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49 <data name="data_group" from_work_dir="Output/mainglm_group/donneesGroupes_mainglm_group.tabular" format="tabular" label="Glm - Group data on ${on_string}"/>
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50 <data name="year_var_group" from_work_dir="Output/mainglm_group/variationsAnnuellesGroupes_mainglm_group.tabular" format="tabular" label="Glm - Group yearly variations data on ${on_string}"/>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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51 <data name="glob_tend_group" from_work_dir="Output/mainglm_group/tendancesGlobalesGroupes_mainglm_group.tabular" format="tabular" label="Glm - Group tendencies on ${on_string}"/>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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52 <data name="plot_year_var_group" from_work_dir="Output/mainglm_group/variationsAnnuellesGroupes_mainglm_group.png" format="png" label="Glm - Group yearly variations plot on ${on_string}"/>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="inputtabSpecies" value="tabSpecies.csv"/>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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57 <param name="input_y_var" value="mainglm_tab_years.tabular"/>
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58 <param name="input_glob_tendencies" value ="mainglm_tab_global.tabular"/>
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59 <param name="advanced" value="simple"/>
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60 <output name="data_group">
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61 <assert_contents>
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62 <has_n_lines n="37"/>
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63 <has_size value="3277" delta="100"/>
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64 </assert_contents>
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65 </output>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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66 <output name="year_var_group">
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67 <assert_contents>
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68 <has_n_lines n="37"/>
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69 <has_size value="1623" delta="100"/>
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70 </assert_contents>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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71 </output>
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72 <output name="glob_tend_group">
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73 <assert_contents>
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74 <has_n_lines n="3"/>
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75 <has_size value="154" delta="20"/>
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76 </assert_contents>
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77 </output>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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78 <output name="plot_year_var_group">
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79 <assert_contents>
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80 <has_text text="PNG"/>
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81 </assert_contents>
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82 </output>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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83 </test>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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84 </tests>
344ccea8292b "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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85 <help><![CDATA[
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86 =================================================
1
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87 STOC Estimate species population variation
0
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88 =================================================
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89
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90 **What it does**
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91
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92
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93
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94 Compute and plot trends of species population by specialization group, using a glm model. The same model than glm per species is used but results are aggregated by specialization group.
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95
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96
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97 |
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98
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99 **Input description**
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100
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101 Two tabular files processed with the STOCs 'Preprocess population data' 'Filter species' on one hand and 'mainglm' tools on the other hand.
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102
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103 One tabular species file, with a `species ID` column and species names.
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104
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105 |
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106
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107 **Output**
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108
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109
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110 Two tabular files are created, they describe global tendencies and yearly variations per groups. One plot of yearly variations per group.
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111 One tabular file describing species with several columns as species ID, species name, species scientific name and specialization status.
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112 |
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113
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114 **Source**
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115
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116 UnPublished script available at http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip
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117 the first version written by Romain Lorrilliere.
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118
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119 ]]></help>
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120 <expand macro="stoceps_bibref" />
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121 </tool>