Mercurial > repos > bcclaywell > microbiome_community_suite
changeset 0:12b4f093e6c4 draft default tip
planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
| author | bcclaywell |
|---|---|
| date | Mon, 12 Oct 2015 16:46:15 -0400 |
| parents | |
| children | |
| files | community.R community.xml cooccurrence.R cooccurrence.xml descriptiveStatistics.R descriptiveStatistics.xml diversityStatistics.R diversityStatistics.xml getAttributeList.R getAttributeList.xml presenceAbsence.R presenceAbsence.xml rankAbundancePlot.R rankAbundancePlot.xml reducedDimensionality.R reducedDimensionality.xml ribbonPlot.R ribbonPlot.xml |
| diffstat | 18 files changed, 840 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/community.R Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,54 @@ +#!/usr/bin/env Rscript + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() + +option_list$CountsFile <- make_option('--CountsFile', type='character') +option_list$SamplesFile <- make_option('--SamplesFile', type='character') +option_list$K <- make_option('--K', type='numeric') +option_list$A <- make_option('--A', type='numeric') +option_list$Transform <- make_option('--Transform', type='character') +option_list$SampleName <- make_option('--SampleName', type='character') +option_list$ColumnClasses <- make_option('--ColumnClasses', type='character') +option_list$OutputFile <- make_option('--OutputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + +suppressPackageStartupMessages(library(microbiomePkg)) + +## function body not needed here, it is in package + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(community, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +})
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/community.xml Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,70 @@ +<tool id="community" name="Community" version="0.0.16"> + <description>'Community' Data Input</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2014-05-02">microbiome_community</requirement> + </requirements> + <command interpreter="Rscript --vanilla">community.R + #if str($CountsFile).strip() != "": + --CountsFile="$CountsFile" + #end if + #if str($SamplesFile).strip() != "": + --SamplesFile="$SamplesFile" + #end if + #if str($K).strip() != "": + --K="$K" + #end if + #if str($A).strip() != "": + --A="$A" + #end if + #if str($Transform).strip() != "": + --Transform="$Transform" + #end if + #if str($SampleName).strip() != "": + --SampleName="$SampleName" + #end if + #if str($ColumnClasses).strip() != "": + --ColumnClasses="$ColumnClasses" + #end if + #if str($OutputFile).strip() != "": + --OutputFile="$OutputFile" + #end if + +2>&1</command> + <inputs> + <param optional="false" name="CountsFile" type="data" help="Name of a CSV file containing OTU samples." label="[required] Counts File"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="false" name="SamplesFile" type="data" help="Name of a CSV file containing sample data." label="[required] Samples File"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="K" type="float" value="0" help="The parameters 'K' and 'A' together define a 'K over A' filter. The filter can be used to include only some taxa. The idea is that a taxonomic entity is only included if at least 'A' reads are present in at least 'K' samples. The default is A = K = 0, i.e., include all taxa. Specify 'K' in the box above." label="K"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="A" type="float" value="0" help="Include only taxa with at least K samples greater than A, as described for the parameter K." label="A"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="Transform" type="select" help="(Optional) A transformation applied to all count data, after the 'K Over A' filter has been run. Possible values include "log" (actually, log(x + .5) to avoid logarithms of zero counts) and "asinh" (inverse hyperboloic sine, a log-like transformation with better behavior near zero)." label="Transform" force_select="FALSE"> + <validator type="empty_field" message="This field is required."/> + <option value="none">none</option> + <option value="log">log</option> + <option value="asinh">asinh</option> + </param> + <param optional="true" name="SampleName" type="text" help="(Optional) Samples File column name containing names by which samples are identified in all subsequent calculations. If two rows have the same Sample Name, then corresponding counts in the Counts File are added together." size="60" label="Sample Name"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="ColumnClasses" type="text" help="(Optional) Comma-separated names specifying how each column is to be represented. There must be as many names, and in the same order, as there are columns in the file. Typical values include: logical, integer, numeric, character, factor, Date. Use 'factor' to indicate a variable with discrete levels, e.g., sex (with levels Male, Female) tissue type (with levels Tumor, Normal), etc. When 'Date' is used, dates should be formatted consistently as year-month-day or year/month/day, e.g., 2014-03-26; poorly formed dates will be converted to 'NA' values." size="60" label="Column Classes"> + <validator type="empty_field" message="This field is required."/> + </param> + </inputs> + <outputs> + <data format="rda" name="OutputFile" label="community.rda"/> + </outputs> + <help> +**Description** + +Input a CSV file of integer-valued counts of each taxon (row) in +each sample (column), and a CSV file of annotations on each +sample. The result is used in down-stream analysis. +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cooccurrence.R Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,50 @@ +#!/usr/bin/env Rscript + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() + +option_list$CommunityFile <- make_option('--CommunityFile', type='character') +option_list$TaxonQuantile <- make_option('--TaxonQuantile', type='numeric') +option_list$Transform <- make_option('--Transform', type='character') +option_list$OutputFile <- make_option('--OutputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + +suppressPackageStartupMessages(library(microbiomePkg)) + +## function body not needed here, it is in package + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(cooccurrence, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +})
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cooccurrence.xml Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,45 @@ +<tool id="cooccurrence" name="Cooccurrence" version="0.0.16"> + <description>Taxonomic Co-occurrence Heatmap</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2014-05-02">microbiome_community</requirement> + </requirements> + <command interpreter="Rscript --vanilla">cooccurrence.R + #if str($CommunityFile).strip() != "": + --CommunityFile="$CommunityFile" + #end if + #if str($TaxonQuantile).strip() != "": + --TaxonQuantile="$TaxonQuantile" + #end if + #if str($Transform).strip() != "": + --Transform="$Transform" + #end if + #if str($OutputFile).strip() != "": + --OutputFile="$OutputFile" + #end if + +2>&1</command> + <inputs> + <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="TaxonQuantile" type="float" value="0" help="(Optional, default 0) Numeric value between 0 and 1, limiting only taxa more frequent than the specified quantile." label="Taxon Quantile"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="Transform" type="select" help="(Optional; default 'none') Character string defining how count data are to be transformed prior to calculation of co-occurrence. Possible values are 'none', 'log1' (log of 1 + the observed count, to allow for zeros in the data), 'asinh' (a log-like transformation that handles zeros more naturally), 'sqrt' (square root, a transformation commonly used for count data)." label="Transform" force_select="FALSE"> + <validator type="empty_field" message="This field is required."/> + <option value="none">none</option> + <option value="log1">log1</option> + <option value="asinh">asinh</option> + <option value="sqrt">sqrt</option> + </param> + </inputs> + <outputs> + <data format="pdf" name="OutputFile" label="cooccurrence.pdf"/> + </outputs> + <help> +**Description** + +Taxonomic co-occurrence across samples, displayed as a heatmap. +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/descriptiveStatistics.R Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,49 @@ +#!/usr/bin/env Rscript + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() + +option_list$CommunityFile <- make_option('--CommunityFile', type='character') +option_list$Attributes <- make_option('--Attributes', type='character') +option_list$OutputFile <- make_option('--OutputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + +suppressPackageStartupMessages(library(microbiomePkg)) + +## function body not needed here, it is in package + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(descriptiveStatistics, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +})
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/descriptiveStatistics.xml Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,36 @@ +<tool id="descriptiveStatistics" name="Descriptive Statistics" version="0.0.16"> + <description>Taxonomic and Sample Descriptive Statistics</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2014-05-02">microbiome_community</requirement> + </requirements> + <command interpreter="Rscript --vanilla">descriptiveStatistics.R + #if str($CommunityFile).strip() != "": + --CommunityFile="$CommunityFile" + #end if + #if str($Attributes).strip() != "": + --Attributes="$Attributes" + #end if + #if str($OutputFile).strip() != "": + --OutputFile="$OutputFile" + #end if + +2>&1</command> + <inputs> + <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="Attributes" type="text" help="Comma-separated names of SamplesFile columns on which descriptive statistics are to be calculated. Example: Nugent_2_group" size="60" label="Attributes"> + <validator type="empty_field" message="This field is required."/> + </param> + </inputs> + <outputs> + <data format="txt" name="OutputFile" label="descriptiveStatistics.txt"/> + </outputs> + <help> +**Description** + +Generate descriptive statistics about taxa and samples present in +a CommunityFile. +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/diversityStatistics.R Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,48 @@ +#!/usr/bin/env Rscript + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() + +option_list$CommunityFile <- make_option('--CommunityFile', type='character') +option_list$OutputFile <- make_option('--OutputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + +suppressPackageStartupMessages(library(microbiomePkg)) + +## function body not needed here, it is in package + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(diversityStatistics, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +})
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/diversityStatistics.xml Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,31 @@ +<tool id="diversityStatistics" name="Diversity Statistics" version="0.0.16"> + <description>Taxonomic Diversity Statistics</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2014-05-02">microbiome_community</requirement> + </requirements> + <command interpreter="Rscript --vanilla">diversityStatistics.R + #if str($CommunityFile).strip() != "": + --CommunityFile="$CommunityFile" + #end if + #if str($OutputFile).strip() != "": + --OutputFile="$OutputFile" + #end if + +2>&1</command> + <inputs> + <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File"> + <validator type="empty_field" message="This field is required."/> + </param> + </inputs> + <outputs> + <data format="csv" name="OutputFile" label="diversityStatistics.csv"/> + </outputs> + <help> +**Description** + +Compute per-sample Shannon, Simpson, Chao1, and ACE summary +statistics of taxonomic diversity. Also report per-sample number +of taxa with non-zero read counts, and total number of reads. +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getAttributeList.R Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,48 @@ +#!/usr/bin/env Rscript + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() + +option_list$CommunityFile <- make_option('--CommunityFile', type='character') +option_list$OutputFile <- make_option('--OutputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + +suppressPackageStartupMessages(library(microbiomePkg)) + +## function body not needed here, it is in package + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(getAttributeList, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +})
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getAttributeList.xml Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,30 @@ +<tool id="getAttributeList" name="Get Attribute List" version="0.0.16"> + <description>Get available attributes from a community file.</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2014-05-02">microbiome_community</requirement> + </requirements> + <command interpreter="Rscript --vanilla">getAttributeList.R + #if str($CommunityFile).strip() != "": + --CommunityFile="$CommunityFile" + #end if + #if str($OutputFile).strip() != "": + --OutputFile="$OutputFile" + #end if + +2>&1</command> + <inputs> + <param optional="false" name="CommunityFile" format="rda" type="data" help="created by the 'community' function." label="[required] Community File"> + <validator type="empty_field" message="This field is required."/> + </param> + </inputs> + <outputs> + <data format="txt" name="OutputFile" label="attributes.txt"/> + </outputs> + <help> +**Description** + +Display available attributes from a community file, for use with +other Microbiome Workflow tools. +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/presenceAbsence.R Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,49 @@ +#!/usr/bin/env Rscript + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() + +option_list$CommunityFile <- make_option('--CommunityFile', type='character') +option_list$Attribute <- make_option('--Attribute', type='character') +option_list$OutputFile <- make_option('--OutputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + +suppressPackageStartupMessages(library(microbiomePkg)) + +## function body not needed here, it is in package + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(presenceAbsence, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +})
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/presenceAbsence.xml Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,35 @@ +<tool id="presenceAbsence" name="Presence Absence" version="0.0.16"> + <description>Taxonomic Presence / Absence Summary and Chi-squared Test</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2014-05-02">microbiome_community</requirement> + </requirements> + <command interpreter="Rscript --vanilla">presenceAbsence.R + #if str($CommunityFile).strip() != "": + --CommunityFile="$CommunityFile" + #end if + #if str($Attribute).strip() != "": + --Attribute="$Attribute" + #end if + #if str($OutputFile).strip() != "": + --OutputFile="$OutputFile" + #end if + +2>&1</command> + <inputs> + <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function" label="[required] Community File"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="Attribute" type="text" help="Name of a sample attribute to summarize presence / absence data. Example: Nugent_2_group" size="60" label="Attribute"> + <validator type="empty_field" message="This field is required."/> + </param> + </inputs> + <outputs> + <data format="csv" name="OutputFile" label="presenceAbsence.csv"/> + </outputs> + <help> +**Description** + +Summarize samples with each taxon present, grouped by factor +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rankAbundancePlot.R Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,52 @@ +#!/usr/bin/env Rscript + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() + +option_list$CommunityFile <- make_option('--CommunityFile', type='character') +option_list$TaxonQuantile <- make_option('--TaxonQuantile', type='numeric') +option_list$Transform <- make_option('--Transform', type='character') +option_list$RelativeAbundance <- make_option('--RelativeAbundance', type='logical') +option_list$Attributes <- make_option('--Attributes', type='character') +option_list$OutputFile <- make_option('--OutputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + +suppressPackageStartupMessages(library(microbiomePkg)) + +## function body not needed here, it is in package + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(rankAbundancePlot, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +})
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rankAbundancePlot.xml Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,57 @@ +<tool id="rankAbundancePlot" name="Rank Abundance Plot" version="0.0.16"> + <description>Rank Abundance of Taxonomic Counts</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2014-05-02">microbiome_community</requirement> + </requirements> + <command interpreter="Rscript --vanilla">rankAbundancePlot.R + #if str($CommunityFile).strip() != "": + --CommunityFile="$CommunityFile" + #end if + #if str($TaxonQuantile).strip() != "": + --TaxonQuantile="$TaxonQuantile" + #end if + #if str($Transform).strip() != "": + --Transform="$Transform" + #end if + #if str($RelativeAbundance).strip() != "": + --RelativeAbundance="$RelativeAbundance" + #end if + #if str($Attributes).strip() != "": + --Attributes="$Attributes" + #end if + #if str($OutputFile).strip() != "": + --OutputFile="$OutputFile" + #end if + +2>&1</command> + <inputs> + <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="TaxonQuantile" type="float" value="0" help="(Optional, default 0) Numeric value between 0 and 1, limiting only taxa more frequent than the specified quantile." label="Taxon Quantile"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="Transform" type="select" help="(Optional; default 'none') Character string defining how count data are to be transformed prior to calculation of co-occurrence. Possible values are 'none', 'log1' (log of 1 + the observed count, to allow for zeros in the data), 'asinh' (a log-like transformation that handles zeros more naturally), 'sqrt' (square root, a transformation commonly used for count data)." label="Transform" force_select="FALSE"> + <validator type="empty_field" message="This field is required."/> + <option value="none">none</option> + <option value="log1">log1</option> + <option value="asinh">asinh</option> + <option value="sqrt">sqrt</option> + </param> + <param optional="true" name="RelativeAbundance" type="boolean" value="FALSE" help="(Optional, default FALSE) When TRUE, scale transformed taxon abundances of each sample to sum to 1." checked="false" label="Relative Abundance"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="Attributes" type="text" help="Provide ribbon(s) identifying samples according to specified attributes." size="60" label="Attributes"> + <validator type="empty_field" message="This field is required."/> + </param> + </inputs> + <outputs> + <data format="pdf" name="OutputFile" label="rankAbundance.pdf"/> + </outputs> + <help> +**Description** + +Rank abundance plots +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reducedDimensionality.R Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,50 @@ +#!/usr/bin/env Rscript + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() + +option_list$CommunityFile <- make_option('--CommunityFile', type='character') +option_list$Attributes <- make_option('--Attributes', type='character') +option_list$OrdinationAlgorithm <- make_option('--OrdinationAlgorithm', type='character') +option_list$OutputFile <- make_option('--OutputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + +suppressPackageStartupMessages(library(microbiomePkg)) + +## function body not needed here, it is in package + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(reducedDimensionality, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +})
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reducedDimensionality.xml Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,42 @@ +<tool id="reducedDimensionality" name="Reduced Dimensionality" version="0.0.16"> + <description>Taxnomic Dimensionality Reduction (Ordination) Plot</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2014-05-02">microbiome_community</requirement> + </requirements> + <command interpreter="Rscript --vanilla">reducedDimensionality.R + #if str($CommunityFile).strip() != "": + --CommunityFile="$CommunityFile" + #end if + #if str($Attributes).strip() != "": + --Attributes="$Attributes" + #end if + #if str($OrdinationAlgorithm).strip() != "": + --OrdinationAlgorithm="$OrdinationAlgorithm" + #end if + #if str($OutputFile).strip() != "": + --OutputFile="$OutputFile" + #end if + +2>&1</command> + <inputs> + <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="Attributes" type="text" help="Comma-separated names of SamplesFile columns on which ribbons are to be plotted. Samples are ordered by the first element of Attributes; Attributes must identify more than 1 SampleFile column. Example: Nugent_3_group, Amsel, Nugent_Lactobacillus, pH, Clue" size="60" label="Attributes"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="OrdinationAlgorithm" type="select" value="MDS" help="Algorithm to use for oridination "PCoA" (Principle Coordinates Analysis), "NMDS" (Non-Metric Multidimensional Scaling), "CA" (Correspondence Analysis), "DPCoA" (Double Principle Components Analysis)." label="Ordination Algorithm" force_select="FALSE"> + <validator type="empty_field" message="This field is required."/> + <option value="MDS">MDS</option> + </param> + </inputs> + <outputs> + <data format="pdf" name="OutputFile" label="reducedDimensionality.pdf"/> + </outputs> + <help> +**Description** + +Reduce dimensionality of taxonomic abundance. +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribbonPlot.R Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,50 @@ +#!/usr/bin/env Rscript + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() + +option_list$CommunityFile <- make_option('--CommunityFile', type='character') +option_list$Attributes <- make_option('--Attributes', type='character') +option_list$ClusteringAlgorithm <- make_option('--ClusteringAlgorithm', type='character') +option_list$OutputFile <- make_option('--OutputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + +suppressPackageStartupMessages(library(microbiomePkg)) + +## function body not needed here, it is in package + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(ribbonPlot, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +})
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribbonPlot.xml Mon Oct 12 16:46:15 2015 -0400 @@ -0,0 +1,44 @@ +<tool id="ribbonPlot" name="Ribbon Plot" version="0.0.16"> + <description>Attribute Ribbon Plot of Clustered Samples</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="2014-05-02">microbiome_community</requirement> + </requirements> + <command interpreter="Rscript --vanilla">ribbonPlot.R + #if str($CommunityFile).strip() != "": + --CommunityFile="$CommunityFile" + #end if + #if str($Attributes).strip() != "": + --Attributes="$Attributes" + #end if + #if str($ClusteringAlgorithm).strip() != "": + --ClusteringAlgorithm="$ClusteringAlgorithm" + #end if + #if str($OutputFile).strip() != "": + --OutputFile="$OutputFile" + #end if + +2>&1</command> + <inputs> + <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="Attributes" type="text" help="Comma-separated names of SamplesFile columns on which ribbons are to be plotted. Samples are ordered by the first element of Attributes; Attributes must identify more than 1 SampleFile column. Example: Nugent_3_group, Amsel, Nugent_Lactobacillus, pH, Clue" size="60" label="Attributes"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="true" name="ClusteringAlgorithm" type="select" help="Algorithm to use for clustering samples, one of "hclust" or 'DirichletMultinomial" (from the DirichletMultinomial package)." label="Clustering Algorithm" force_select="FALSE"> + <validator type="empty_field" message="This field is required."/> + <option value="hclust">hclust</option> + <option value="DirichletMultinomial">DirichletMultinomial</option> + </param> + </inputs> + <outputs> + <data format="svg" name="OutputFile" label="ribbonPlot.svg"/> + </outputs> + <help> +**Description** + +Attributes of samples as heat maps, with samples clustered by one +of several algorithms +</help> +</tool>