# HG changeset patch
# User sblanck
# Date 1460547602 14400
# Node ID 27ffdb4958523c785b359534157bf811eb63e9a3
Imported from capsule None
diff -r 000000000000 -r 27ffdb495852 AffyQCnormalization.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/AffyQCnormalization.xml Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,44 @@
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+ Quality control and normalization of affymetric expression data
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+ sblanck/testtool:latest
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+
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+ /galaxy-tools/stderr_wrapper.py Rscript
+ /galaxy-tools/transcriptomics/AffyQCnormalization/AffyQCnormalization.R
+ #for $input in $inputs
+ "${input}"
+ "${input.name}"
+ #end for
+ "${normalization}"
+ $result_export_eset
+ $result_html
+ $result_html.files_path
+ /galaxy-tools/transcriptomics/AffyQCnormalization/AffyQCnormalization_tpl.html
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\ No newline at end of file
diff -r 000000000000 -r 27ffdb495852 CustomAnalyse.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CustomAnalyse.xml Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,64 @@
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+ Custom Analyse
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+ sblanck/testtool:latest
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+
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+ /galaxy-tools/stderr_wrapper.py Rscript
+ /galaxy-tools/transcriptomics/CustomAnalyse/CustomAnalyse.R
+ #for $input in $inputs
+ "${input}"
+ "${input.name}"
+ #end for
+ "${target}"
+ "${selectCondition1}"
+ "${selectCondition2}"
+ $result_export_eset
+ $result_export_conditions
+ $result_html
+ $result_html.files_path
+ /galaxy-tools/transcriptomics/CustomAnalyse/CustomAnalyse_tpl.html
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+ NOTE: This wrapper performs p-value combination from multiples studies with the same probes. If you need to normalize your data, use "matrix_normalisation" tool on each file. Then, use "Merge Standard datasets(copied)" tool to make a multiple file dataset.
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diff -r 000000000000 -r 27ffdb495852 GEOAnalyse.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GEOAnalyse.xml Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,41 @@
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+ GEOAnalyse wrapper
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+ sblanck/testtool:latest
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+
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+ /galaxy-tools/stderr_wrapper.py Rscript
+ /galaxy-tools/transcriptomics/GEOanalyse/GEOAnalyse.R
+ "${rdataset}"
+ "${selectCondition}"
+ $result_html
+ $result_html.files_path
+ /galaxy-tools/transcriptomics/GEOanalyse/GEOAnalyse_tpl.html
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+ NOTE: This metaMA wrapper performs p-value combination from multiples studies with the same probes. If you need to normalize your data, use "matrix_normalisation" tool on each file. Then, use "Merge Standard datasets(copied)" tool to make a multiple file dataset.
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diff -r 000000000000 -r 27ffdb495852 GEOQuery.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GEOQuery.xml Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,27 @@
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+ GEOQuery wrapper
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+ sblanck/testtool:latest
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+ /galaxy-tools/stderr_wrapper.py Rscript /galaxy-tools/transcriptomics/GEOquery/GEOQuery.R $GEOQueryID $GEOQueryData $GEOQueryRData $conditions
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diff -r 000000000000 -r 27ffdb495852 MetaMA.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MetaMA.xml Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,46 @@
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+ metaMA wrapper
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+ sblanck/testtool:latest
+
+
+
+ /galaxy-tools/stderr_wrapper.py Rscript
+ /galaxy-tools/transcriptomics/MetaMA/MetaMA.R
+ #for $currentInput in $inputList
+ "${currentInput.rdataset}"
+ "${currentInput.selectCondition}"
+ #end for
+ $result_html
+ $result_html.extra_files_path
+ /galaxy-tools/transcriptomics/MetaMA/MetaMa_tpl.html
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+ NOTE: This metaMA wrapper performs p-value combination from multiples studies with the same probes. If you need to normalize your data, use "matrix_normalisation" tool on each file. Then, use "Merge Standard datasets(copied)" tool to make a multiple file dataset.
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diff -r 000000000000 -r 27ffdb495852 MetaRNAseq.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MetaRNAseq.xml Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,53 @@
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+ metaRNASeq wrapper
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+ sblanck/testtool:latest
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+
+
+ /galaxy-tools/stderr_wrapper.py Rscript
+ /galaxy-tools/transcriptomics/MetaRNASeq/MetaRNASeq.R
+ #for $currentInput in $inputList
+ "${currentInput}"
+ "${currentInput.name}"
+ #end for
+ $comparison
+ $method
+ $mod
+ $top_table
+ $diagnostic_html
+ "$diagnostic_html.files_path"
+ /galaxy-tools/transcriptomics/MetaRNAseq/MetaRNASeq_tpl.html
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+ ^\w+,\w+$
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+ NOTE: This metaRNASeq Galaxy tool can only be run on counts files.
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diff -r 000000000000 -r 27ffdb495852 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,4 @@
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