comparison mainglm.xml @ 1:a961be0a964f draft default tip

"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"

0:df3ce23d0d23

<tool id="stoceps_glm" name="Estimate temporal population evolution" version="@VERSION@">
    <description>by species</description>
    <macros>
        <import>stoceps_macros.xml</import>
    </macros>
    <expand macro="mainglm_requirements"/>

            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
=================================================
STOC Estimate species population evolution
=================================================

**What it does**

Compute and plot evolution of species population, using a glm model.

|

**Input description**

**Source**

UnPublished script available at http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip
the first version written by Romain Lorrilliere

Original script information:

Estimate temporal evolution of population per species - ExeMainGlmGalaxy.r
This script analyse the temporal evolution of species population and create graphical vizualisation.

Script needs the followings inputs :
 - stoc or community data filtered with at least 4 columns: year, site, species, and abundance with 0. Corresponding to "observed" or predicted 0 abundance. May come from the tools "Preprocess population data for evolution trend analyzes" (ExemakeTableAnalyseGalaxy.r) followed by "Filter species with rare and low abundances" (ExeFilteringRareLowabundSPGalaxy.r).
 - species details file with name and indicator status file with at least 2 columns: the species name or species ID (found in the community data or in stoc data) and his status as indicator species
 - file that stocks functions : "FunctTrendSTOCGalaxy.r"


Arguments are :
 - spExclude: list of species (using the the species name or ID) that you want to exclude
 - assessIC : compute and show confidence interval in plots (TRUE / FALSE)
 - analysis custom id


How to execute, eg :
 # all files are available in github repo
 #Exec id=mainglm, return IC on plot, no species excluded
 $ Rscript ExeMainGlmGalaxy.r' Datafilteredfortrendanalysis.tabular tabSpecies.csv 'mainglm' '' 'TRUE' FunctTrendSTOCGalaxy.r


Outputs are created in an Output repo :
GLM gives 1 graph per species and 2 tables:
- nameofspecies_id.png (one plot per species)
- tendanceGlobalEspece_id.tabular
- variationsAnnuellesEspece_id.tabular


R library needed
r-lme4  version 1.1.18.1
r-ggplot2  version 3.0.0
r-speedglm  version 0.3.2
r-arm  version 1.10.1
r-reshape  version 0.8.8
r-data.table  version 1.12.0
r-reshape2   version 1.4.3
  ]]></help>
  <expand macro="stoceps_bibref" />
</tool>

1:a961be0a964f

<tool id="stoceps_glm" name="Estimate temporal population variation" version="@VERSION@">
    <description>by species</description>
    <macros>
        <import>stoceps_macros.xml</import>
    </macros>
    <expand macro="mainglm_requirements"/>

            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
=================================================
STOC Estimate species population variation
=================================================

**What it does**

Compute and plot trends of species population, using a glm model of formula : abundance ~ site + year. Testing the effect of site and year on abundance with quasipoisson distribution.

|

**Input description**

**Source**

UnPublished script available at http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip
the first version written by Romain Lorrilliere

  ]]></help>
  <expand macro="stoceps_bibref" />
</tool>