Mercurial > repos > fubar > edger_test
changeset 49:c4f8c9a00c0e draft
Uploaded
| author | fubar |
|---|---|
| date | Fri, 26 Jul 2013 22:47:38 -0400 |
| parents | 91e77df18a7f |
| children | c7d173c236f4 |
| files | rgedgeR/rgedgeRpaired.xml rgedgeR/tool_dependencies.xml |
| diffstat | 2 files changed, 7 insertions(+), 57 deletions(-) [+] |
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--- a/rgedgeR/rgedgeRpaired.xml Fri Jul 26 22:04:58 2013 -0400 +++ b/rgedgeR/rgedgeRpaired.xml Fri Jul 26 22:47:38 2013 -0400 @@ -2,7 +2,7 @@ <description>models using BioConductor packages</description> <requirements> <requirement type="package" version="2.12">biocbasics</requirement> - <requirement type="package" version="3.0.1">package_r3</requirement> + <requirement type="package" version="3.0.1">r3</requirement> </requirements> <command interpreter="python"> @@ -76,45 +76,6 @@ <option value="F" selected="true">Do not run VOOM</option> <option value="T">Run VOOM</option> </param> - <conditional name="camera"> - <param name="doCamera" type="select" label="Run the edgeR implementation of Camera GSEA for up/down gene sets" - help="If yes, you can choose a set of genesets to test and/or supply a gmt format geneset collection from your history"> - <option value="F" selected="true">Do not run GSEA tests with the Camera algorithm</option> - <option value="T">Run GSEA tests with the Camera algorithm</option> - </param> - <when value="T"> - <conditional name="gmtSource"> - <param name="refgmtSource" type="select" - label="Use a gene set (.gmt) from your history and/or use a built-in (MSigDB etc) gene set"> - <option value="indexed" selected="true">Use a built-in gene set</option> - <option value="history">Use a gene set from my history</option> - <option value="both">Add a gene set from my history to a built in gene set</option> - </param> - <when value="indexed"> - <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis"> - <options from_data_table="gseaGMT_3.1"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No GMT v3.1 files are available - please install them"/> - </options> - </param> - </when> - <when value="history"> - <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" /> - </when> - <when value="both"> - <param name="ownGMT" type="data" format="gseagmt" label="Select a Gene Set from your history" /> - <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis"> - <options from_data_table="gseaGMT_4"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No GMT v4 files are available - please fix tool_data_table and loc files"/> - </options> - </param> - </when> - </conditional> - </when> - <when value="F"> - </when> - </conditional> <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control" help="Conventional default value of 0.05 recommended"/> <param name="fdrtype" type="select" label="FDR (Type II error) control method" @@ -145,7 +106,6 @@ <param name='doedgeR' value='T' /> <param name='doVoom' value='T' /> <param name='doDESeq2' value='T' /> - <param name='doCamera' value='T' /> <param name='fdrtype' value='fdr' /> <param name='edgeR_priordf' value="8" /> <param name='fdrthresh' value="0.05" /> @@ -691,7 +651,7 @@ history_gmt="" doDESeq2 = $DESeq2.doDESeq2 # make these T or F doVoom = $doVoom -doCamera = $camera.doCamera +doCamera = F doedgeR = $edgeR.doedgeR edgeR_priordf = 0 @@ -702,17 +662,6 @@ edgeR_priordf = $edgeR.edgeR_priordf #end if -#if $camera.doCamera == 'T' -#if $camera.gmtSource.refgmtSource == "indexed" or $camera.gmtSource.refgmtSource == "both": - builtin_gmt = "${camera.gmtSource.builtinGMT.fields.path}" -#end if -#if $camera.gmtSource.refgmtSource == "history" or $camera.gmtSource.refgmtSource == "both": - history_gmt = "${camera.gmtSource.ownGMT}" - history_gmt_name = "${camera.gmtSource.ownGMT.name}" - #end if -#end if - - Out_Dir = "$html_file.files_path" Input = "$input1"
--- a/rgedgeR/tool_dependencies.xml Fri Jul 26 22:04:58 2013 -0400 +++ b/rgedgeR/tool_dependencies.xml Fri Jul 26 22:47:38 2013 -0400 @@ -1,21 +1,22 @@ <?xml version="1.0"?> <tool_dependency> - <package name="package_r3" version="3.0.1"> - <repository changeset_revision="6f249fadd4ec" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <package name="r3" version="3.0.1"> + <repository changeset_revision="1ffaf8412079" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> <package name="biocbasics" version="2.12"> <install version="1.0"> <actions> <action type="set_environment_for_install"> - <repository changeset_revision="6f249fadd4ec" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <repository changeset_revision="1ffaf8412079" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> <package name="r3" version="3.0.1" /> </repository> </action> <action type="make_directory">$INSTALL_DIR</action> <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2','gplots')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" >> $INSTALL_DIR/runme.R</action> <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T)" >> $INSTALL_DIR/runme.R</action> <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> </actions>