Mercurial > repos > iuc > goseq
diff goseq.xml @ 3:783e8b70b047 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 46c4278d292ab4d76dc5f3f74c3109c3179be7ef
| author | iuc |
|---|---|
| date | Mon, 24 Sep 2018 06:29:03 -0400 |
| parents | ab492df30cdf |
| children | ae39895af5fe |
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--- a/goseq.xml Mon Oct 23 11:19:12 2017 -0400 +++ b/goseq.xml Mon Sep 24 06:29:03 2018 -0400 @@ -1,12 +1,14 @@ -<tool id="goseq" name="goseq" version="1.26.0"> +<tool id="goseq" name="goseq" version="1.30.0"> <description>tests for overrepresented gene categories</description> <requirements> - <requirement type="package" version="1.3.2">r-optparse</requirement> - <requirement type="package" version="1.26.0">bioconductor-goseq</requirement> - <requirement type="package" version="3.3.0">bioconductor-org.hs.eg.db</requirement> - <requirement type="package" version="3.4.0">bioconductor-org.dm.eg.db</requirement> - <requirement type="package" version="3.4.1">bioconductor-org.dr.eg.db</requirement> - <requirement type="package" version="3.4.0">bioconductor-org.mm.eg.db</requirement> + <requirement type="package" version="1.6.0">r-optparse</requirement> + <requirement type="package" version="1.30.0">bioconductor-goseq</requirement> + <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> + <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement> + <requirement type="package" version="3.5.0">bioconductor-org.dr.eg.db</requirement> + <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> + <requirement type="package" version="0.7.6">r-dplyr</requirement> + <requirement type="package" version="3.0.0">r-ggplot2</requirement> </requirements> <stdio> <regex match="Execution halted" @@ -23,7 +25,7 @@ description="An undefined error occured, please check your input carefully and contact your administrator." /> </stdio> <version_command><![CDATA[ -echo $(R --version | grep version | grep -v GNU)", goseq version" $(R --vanilla --slave -e "library(goseq); cat(sessionInfo()\$otherPkgs\$goseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ") +echo $(R --version | grep version | grep -v GNU)", goseq version" $(R --vanilla --slave -e "library(goseq); cat(sessionInfo()\$otherPkgs\$goseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", dplyr version" $(R --vanilla --slave -e "library(dplyr); cat(sessionInfo()\$otherPkgs\$dplyr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") ]]></version_command> <command><![CDATA[ Rscript '$__tool_directory__/goseq.r' @@ -51,11 +53,15 @@ --make_plots '$out.make_plots' --length_bias_plot '$length_bias_plot' --sample_vs_wallenius_plot '$sample_vs_wallenius_plot' + --rdata '$out.rdata_out' - --p_adj_method '$adv.p_adj_method' --use_genes_without_cat '$adv.use_genes_without_cat' +#if $out.topgo_plot: + --top_plot '$out.topgo_plot' +#end if + ]]></command> <!-- Input Files--> @@ -100,6 +106,7 @@ <!-- Output Options --> <section name="out" title="Output Options"> + <param name="topgo_plot" type="boolean" checked="false" label="Output Top GO terms plot?" help="Output a PDF plot of the Top 10 over-represented GO terms. Default: No" /> <param name="make_plots" type="boolean" checked="false" label="Produce diagnostic plots?" help="This will produce the length bias (PWF) plot. If both sampling and wallenius methods are selected, it will also produce a plot comparing their p-values. These plots may help you compare the different p-value estimation methods that goseq can use. Default: No" /> <param name="rdata_out" type="boolean" checked="false" label="Output RData file?" help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No" /> </section> @@ -120,7 +127,7 @@ <outputs> <data name="wallenius_tab" format="tabular" label="${tool.name} on ${on_string}: Ranked category list - Wallenius method"> - <filter>methods['wallenius]'</filter> + <filter>methods['wallenius']</filter> </data> <data name="sampling_tab" format="tabular" label="${tool.name} on ${on_string}: Ranked category list - Sampling method"> <filter>methods['repcnt'] != 0</filter> @@ -139,9 +146,23 @@ <data name="rdata" format="rdata" from_work_dir="goseq_analysis.RData" label="${tool.name} on ${on_string}: RData file"> <filter>out['rdata_out']</filter> </data> + <data name="top_plot" format="pdf" from_work_dir="top10.pdf" label="${tool.name} on ${on_string}: Top over-represented GO terms plot"> + <filter>methods['wallenius']</filter> + <filter>out['topgo_plot']</filter> + </data> </outputs> <tests> + <!-- Ensure top plot is output --> + <test expect_num_outputs="2"> + <param name="dge_file" value="dge_list.tab" ftype="tabular" /> + <param name="length_file" value="gene_length.tab" ftype="tabular" /> + <param name="catSource" value="history" /> + <param name="category_file" value="category.tab" ftype="tabular" /> + <param name="use_genes_without_cat" value="true" /> + <param name="topgo_plot" value="true" /> + <output name="top_plot" ftype="pdf" file="topgo.pdf" compare="sim_size"/> + </test> <!-- Ensure Wallenius table is output --> <test expect_num_outputs="1"> <param name="dge_file" value="dge_list.tab" ftype="tabular" /> @@ -149,7 +170,12 @@ <param name="catSource" value="history" /> <param name="category_file" value="category.tab" ftype="tabular" /> <param name="use_genes_without_cat" value="true" /> - <output name="wallenius_tab" file="wal.tab" compare="contains" /> + <output name="wallenius_tab"> + <assert_contents> + <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> + <has_text_matching expression="GO:0000278.*0.01" /> + </assert_contents> + </output> </test> <!-- Ensure getting GO categories works --> <test expect_num_outputs="1"> @@ -159,7 +185,12 @@ <param name="genome" value="hg38" /> <param name="gene_id" value="ensGene" /> <param name="use_genes_without_cat" value="true" /> - <output name="wallenius_tab" ftype="tabular" file="getgo.hg38.tab" compare="contains"/> + <output name="wallenius_tab"> + <assert_contents> + <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> + <has_text_matching expression="GO:0005576.*5.2" /> + </assert_contents> + </output> </test> <!-- Ensure getting GO categories for another genome (zebrafish) works --> <test expect_num_outputs="1"> @@ -169,7 +200,12 @@ <param name="genome" value="danRer10"/> <param name="gene_id" value="ensGene" /> <param name="use_genes_without_cat" value="true" /> - <output name="wallenius_tab" ftype="tabular" file="getgo.danRer10.tab" compare="contains"/> + <output name="wallenius_tab"> + <assert_contents> + <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> + <has_text_matching expression="GO:0031324.*0.08" /> + </assert_contents> + </output> </test> <!-- Ensure length bias plot works --> <test expect_num_outputs="2"> @@ -277,7 +313,7 @@ **Outputs** * This tool outputs a tabular file containing a ranked list of gene categories, similar to below. The default output is the Wallenius method table. If the Sampling and/or Hypergeometric methods are also selected, additional tables are produced. -* Optionally, this tool can also output some diagnostic plots and an RData file, see **Output Options** above. +* Optionally, this tool can also output a plot of the top 10 over-represented categories, some diagnostic plots and an RData file, see **Output Options** above. Example: