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aurora_wgcna.xml |
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| diff -r 66ef158fa85c -r c18d0db68d51 aurora_wgcna.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/aurora_wgcna.xml Fri Nov 22 19:45:05 2019 -0500 |
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| b'@@ -0,0 +1,306 @@\n+<tool id="aurora_wgcna" name="Aurora Galaxy WGCNA" version="1.0.0">\n+ <description>\n+ Identify gene co-expression network modules using WGCNA.\n+ </description>\n+ <requirements>\n+ <requirement type="package" version="2.7.3">pandoc</requirement>\n+ <requirement type="package" version="1.20.3">r-getopt</requirement>\n+ <requirement type="package" version="1.12">r-rmarkdown</requirement>\n+ <requirement type="package" version="1.8.4">r-plyr</requirement>\n+ <requirement type="package" version="0.10">r-dt</requirement>\n+ <requirement type="package" version="0.4.0">r-htmltools</requirement>\n+ <requirement type="package" version="3.2.1">r-ggplot2</requirement>\n+ <requirement type="package" version="1.4.3">r-reshape2</requirement>\n+ <requirement type="package" version="6.0_83">r-caret</requirement>\n+ <requirement type="package" version="1.68">r-wgcna</requirement>\n+ </requirements>\n+ <stdio>\n+ <regex match="Execution halted"\n+ source="both"\n+ level="fatal"\n+ description="Execution halted." />\n+ <regex match="Error in"\n+ source="both"\n+ level="fatal"\n+ description="An undefined error occured, please check your intput carefully and contact your administrator." />\n+ <regex match="Fatal error"\n+ source="both"\n+ level="fatal"\n+ description="An undefined error occured, please check your intput carefully and contact your administrator." />\n+ </stdio>\n+ <command>\n+ <![CDATA[\n+ export TOOL_INSTALL_DIR=\'${__tool_directory__}\' &&\n+\n+ Rscript \'${__tool_directory__}/aurora_wgcna_render.R\'\n+ -e $expression_data\n+ -s $min_cluster_size\n+ -b $block_size\n+ -j $hard_threshold\n+ #if $trait_info.trait_data\n+ -t $trait_info.trait_data\n+ -c $trait_info.sname_col\n+ #if $trait_info.missing_value2\n+ -o "$trait_info.missing_value2"\n+ #else \n+ -o "NA"\n+ #end if\n+ #if $trait_info.one_hot_cols\n+ -y $trait_info.one_hot_cols\n+ #end if\n+ #if $trait_info.ignore_cols\n+ -x $trait_info.ignore_cols\n+ #end if\n+ #end if\n+ #if $height_cut\n+ -h $height_cut\n+ #end if\n+ #if $power\n+ -p $power\n+ #end if\n+ -l $render_log_file\n+ -a $r_data\n+ -k $gene_module_file\n+ -w $network_edges_file\n+ -g $gene_association_file\n+ -m $module_association_file\n+ -q $module_association_report\n+ -r $network_construction_report\n+ -z $updated_trait_matrix\n+ -d $filtered_GEM\n+ -i $missing_value1\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param\n+ type="data"\n+ name="expression_data"\n+ format="csv"\n+ optional="false"\n+ label="Gene expression data"\n+ help="The gene expression data is an n x m matrix where n rows are the genes, m columns are the samples and the elements represent gene expression levels (derived either from Microarray or RNA-Seq). The matrix should be stored in a comma-separated (CSV) file and it must have a header. The gene names must appear as the first column of data in the file."\n+ />\n+ <param\n+ type="text"\n+ value="NA"\n+ name="missing_value1"\n+ optional="false"\n+ label="Missing Value Identifier"\n+ help="Within the gene expression data some genes may have missing values. If so, please indicate the text that is used to identify a missing value. Some common examples include: NA, 0.0, 0, -Inf. Any expression level that exactly matches the value provided wil'..b' format="pdf"\n+ label="module_association_report.pdf">\n+ <filter>trait_data != None</filter>\n+ </data>\n+ <data\n+ name="gene_association_file"\n+ format="csv"\n+ label="gene_association.csv">\n+ <filter>trait_data != None</filter>\n+ </data>\n+ <data\n+ name="module_association_file"\n+ format="csv"\n+ label="module_association.csv">\n+ <filter>trait_data != None</filter>\n+ </data>\n+ <data\n+ name="updated_trait_matrix"\n+ format="csv"\n+ label="updated_trait_matrix.csv">\n+ <filter>trait_data != None</filter>\n+ </data>\n+ <data\n+ name="render_log_file"\n+ format="txt"\n+ label="render_log_file"\n+ hidden="false"\n+ />\n+ <data\n+ name="r_data"\n+ format="rdata"\n+ label="aurora_wgcna.RData"\n+ hidden="true"\n+ />\n+ <collection name="figures" type="list" label="Figures">\n+ <discover_datasets \n+ pattern="__designation_and_ext__" \n+ directory="figures" \n+ visible="false" />\n+ </collection>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name=\'expression_data\' value="LiverFemale3600.gem.csv"/>\n+ <output name="gene_module_file" file="gene_module.csv"/>\n+ <output name="network_edges_file" file="network_edges.txt"/>\n+ <output name="network_construction_report" file="network_construction_report.html"/>\n+ </test>\n+ <test>\n+ <param name=\'expression_data\' value="LiverFemale3600.gem.csv"/>\n+ <param name=\'trait_data\' value="ClinicalTraits.csv"/>\n+ <output name="gene_module_file" file="gene_module.csv"/>\n+ <output name="network_edges_file" file="network_edges.txt"/>\n+ <output name="gene_association_file" file="gene_association_file.csv"/>\n+ <output name="module_association_file" file="module_association_file.csv"/>\n+ <output name="module_association_report" file="module_association_report.html"/>\n+ <output name="network_construction_report" file="network_construction_report.html"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ This tool is a wrapper for the WGCNA R library. Please see the online\n+ WGCNA tutorial for further details.\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="bibtex">\n+ @article{langfelder2008wgcna,\n+ title={WGCNA: an R package for weighted correlation network analysis},\n+ author={Langfelder, Peter and Horvath, Steve},\n+ journal={BMC bioinformatics},\n+ volume={9},\n+ number={1},\n+ pages={559},\n+ year={2008},\n+ publisher={BioMed Central}\n+ }\n+ </citation>\n+ <citation type="bibtex">\n+ @article{allaire2016rmarkdown,\n+ title={rmarkdown: Dynamic Documents for R, 2016},\n+ author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},\n+ journal={R package version 0.9},\n+ volume={6},\n+ year={2016}\n+ }\n+ </citation>\n+ <citation type="bibtex">\n+ @book{xie2015dynamic,\n+ title={Dynamic Documents with R and knitr},\n+ author={Xie, Yihui},\n+ volume={29},\n+ year={2015},\n+ publisher={CRC Press}\n+ }\n+ </citation>\n+ <citation type="bibtex">\n+ @misc{dt2016,\n+ title = {DT: A Wrapper of the JavaScript Library \'DataTables\'},\n+ author = {Yihui Xie},\n+ year = {2016},\n+ note = {R package version 0.2},\n+ url = {https://CRAN.R-project.org/package=DT},\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n' |