# HG changeset patch
# User lain
# Date 1606310588 0
# Node ID eb7756ab1cbd78b3c4ff808253878002f13d26f0
# Parent 1c2ce385b84e52c1413923943b6eb540ff829db6
" master branch Updating"
diff -r 1c2ce385b84e -r eb7756ab1cbd XSeekerPreparator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/XSeekerPreparator.xml Wed Nov 25 13:23:08 2020 +0000
@@ -0,0 +1,340 @@
+
+ Prepare RData file from CAMERA to be visualized in XSeeker
+
+
+ operation_1812
+ operation_0335
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+ R_SCRIPT_PATH
+ R
+ optparse
+ xcms
+ blob
+ fst
+ stringr
+ DBModelR
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+ R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R' -v
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+tryCatch({
+ DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
+}, error=function(e) {
+ stop("Please, install DBModelR before you source this file.")
+})
+
+list(
+ adduct=DBModelR::ModelDefinition(
+ table="adduct",
+ fields=list(
+ name="TEXT",
+ mass="FLOAT",
+ charge="INTEGER",
+ multi="INTEGER",
+ formula_add="TEXT",
+ formula_ded="TEXT",
+ sign="TEXT",
+ oidscore="INTEGER",
+ quasi="INTEGER",
+ ips="FLOAT"
+ )
+ ),
+ cluster=DBModelR::ModelDefinition(
+ table="cluster",
+ fields=list(
+ clusterID="INTEGER",
+ formula="TEXT",
+ annotation="TEXT",
+ coeff="FLOAT",
+ r_squared="FLOAT",
+ charge="INTEGER",
+ mean_rt="FLOAT",
+ score="FLOAT",
+ deviation="FLOAT",
+ status="TEXT",
+ adduct="TEXT",
+ curent_group="INTEGER",
+ pc_group="INTEGER",
+ align_group="INTEGER",
+ xcms_group="INTEGER"
+ ),
+ one=list("sample", "compound")
+ ),
+ compound=DBModelR::ModelDefinition(
+ table="compound",
+ fields=list(
+ name="TEXT",
+ common_name="TEXT",
+ formula="TEXT",
+ charge="INTEGER",
+ date="TEXT",
+ mz="FLOAT"
+ )
+ ),
+ feature=DBModelR::ModelDefinition(
+ table="feature",
+ fields=list(
+ featureID="INTEGER",
+ mz="FLOAT",
+ mz_min="FLOAT",
+ mz_max="FLOAT",
+ rt="FLOAT",
+ rt_min="FLOAT",
+ rt_max="FLOAT",
+ int_o="FLOAT",
+ int_b="FLOAT",
+ max_o="FLOAT",
+ iso="TEXT",
+ abundance="FLOAT"
+ ),
+ one=list("cluster")
+ ),
+ instrument=DBModelR::ModelDefinition(
+ table="instrument",
+ fields=list(
+ model="TEXT",
+ manufacturer="TEXT",
+ analyzer="TEXT",
+ detector_type="TEXT",
+ ion_source="TEXT"
+ )
+ ),
+ instrument_config=DBModelR::ModelDefinition(
+ table="instrument_config",
+ fields=list(
+ resolution="TEXT",
+ agc_target="TEXT",
+ maximum_IT="TEXT",
+ number_of_scan_range="TEXT",
+ scan_range="TEXT",
+ version="TEXT"
+ )
+ ),
+ project=DBModelR::ModelDefinition(
+ table="project",
+ fields=list(
+ name="TEXT",
+ comment="TEXT"
+ ),
+ one=list("sample")
+ ),
+ sample=DBModelR::ModelDefinition(
+ table="sample",
+ fields=list(
+ name="TEXT",
+ path="TEXT",
+ polarity="TEXT",
+ kind="TEXT", ## rdata or mxml or enriched_rdata
+ raw="BLOB"
+ ),
+ one=list(
+ "peak_picking_parameters",
+ "pairing_parameters",
+ "alignmenmt_parameters",
+ "camera_parameters",
+ "instrument",
+ "instrument_config",
+ "software",
+ "smol_xcms_set"
+ )
+ ),
+ smol_xcms_set=DBModelR::ModelDefinition(
+ table="smol_xcms_set",
+ fields=list(
+ raw="BLOB"
+ )
+ ),
+ software=DBModelR::ModelDefinition(
+ table="software",
+ fields=list(
+ name="TEXT",
+ version="TEXT"
+ )
+ ),
+ peak_picking_parameters=DBModelR::ModelDefinition(
+ table="peak_picking_parameters",
+ fields=list(
+ ppm="FLOAT",
+ peakwidth="TEXT",
+ snthresh="TEXT",
+ prefilterStep="TEXT",
+ prefilterLevel="TEXT",
+ mzdiff="TEXT",
+ fitgauss="TEXT",
+ noise="TEXT",
+ mzCenterFun="TEXT",
+ integrate="INTEGER",
+ firstBaselineCheck="TEXT",
+ snthreshIsoROIs="TEXT",
+ maxCharge="INTEGER",
+ maxIso="INTEGER",
+ mzIntervalExtension="TEXT"
+ )
+ ),
+ alignmenmt_parameters=DBModelR::ModelDefinition(
+ table="alignmenmt_parameters",
+ fields=list(
+ binSize="TEXT",
+ centerSample="TEXT",
+ response="TEXT",
+ distFun="TEXT",
+ gapInit="TEXT",
+ gapExtend="TEXT",
+ factorDiag="TEXT",
+ factorGap="TEXT",
+ localAlignment="INTEGER",
+ initPenalty="TEXT",
+ bw="TEXT",
+ minFraction="TEXT",
+ minSamples="TEXT",
+ maxFeatures="TEXT"
+ )
+ )
+)
+
+
+
diff -r 1c2ce385b84e -r eb7756ab1cbd convert/.gitignore
--- a/convert/.gitignore Tue Nov 24 18:57:10 2020 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-*
\ No newline at end of file
diff -r 1c2ce385b84e -r eb7756ab1cbd galaxy/tools/LC-MSMS/XSeekerPreparator.xml
--- a/galaxy/tools/LC-MSMS/XSeekerPreparator.xml Tue Nov 24 18:57:10 2020 +0000
+++ b/galaxy/tools/LC-MSMS/XSeekerPreparator.xml Wed Nov 25 13:23:08 2020 +0000
@@ -1,6 +1,6 @@
-
Prepare RData file from CAMERA to be visualized in XSeeker
@@ -12,9 +12,6 @@
R_SCRIPT_PATH
-
R
optparse
xcms