Corrected arguments for retrieving galaxyPath and sampleName + Remove…

…d the correct number of sample columns in tsv output.
workflow4metabolomics · Oct 23, 2024 · da3a0af · da3a0af
1 parent 572667c
commit da3a0af
Show file tree

Hide file tree

Showing 8 changed files with 24 additions and 24 deletions.
diff --git a/tools/camera/CAMERA_findAdducts.R b/tools/camera/CAMERA_findAdducts.R
@@ -23,8 +23,8 @@ args <- list(
   convertRTMinute = as.logical(args_vec[10]), # TRUE - FALSE
   numDigitsMZ = as.numeric(args_vec[11]), # Number of digits MZ
   numDigitsRT = as.numeric(args_vec[12]), # Number of digits RT
-  singlefile_galaxyPath = args_vec[13], # @COMMAND_FILE_LOAD@
-  singlefile_sampleName = args_vec[14] # @COMMAND_FILE_LOAD@
+  singlefile_galaxyPath = args_vec[14], # @COMMAND_FILE_LOAD@
+  singlefile_sampleName = args_vec[16] # @COMMAND_FILE_LOAD@
 )
 
 # Check if the 'rules' argument in 'args' is NULL
@@ -198,7 +198,7 @@ ncols <- length(colnames(peakList))
 sample_cols <- length(xa@sample) # Number of samples
 
 # Indices for the columns of interest
-main_cols <- 1:(ncols - (3 + sample_cols)) # Main columns before sample columns
+main_cols <- 1:(ncols - (6 + sample_cols)) # Main columns before sample columns
 tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
 
 # Combine the selected columns from matgrp with the group names

diff --git a/tools/camera/CAMERA_findIsotopes.R b/tools/camera/CAMERA_findIsotopes.R
@@ -22,8 +22,8 @@ args <- list(
   convertRTMinute = as.logical(args_vec[9]), # TRUE - FALSE
   numDigitsMZ = as.numeric(args_vec[10]), # Number of digits MZ
   numDigitsRT = as.numeric(args_vec[11]), # Number of digits RT
-  singlefile_galaxyPath = args_vec[12], # @COMMAND_FILE_LOAD@
-  singlefile_sampleName = args_vec[13] # @COMMAND_FILE_LOAD@
+  singlefile_galaxyPath = args_vec[13], # @COMMAND_FILE_LOAD@
+  singlefile_sampleName = args_vec[15] # @COMMAND_FILE_LOAD@
 )
 
 print("Converted arguments:")
@@ -196,7 +196,7 @@ ncols <- length(colnames(peakList))
 sample_cols <- length(xa@sample) # Number of samples
 
 # Indices for the columns of interest
-main_cols <- 1:(ncols - (3 + sample_cols)) # Main columns before sample columns
+main_cols <- 1:(ncols - (6 + sample_cols)) # Main columns before sample columns
 tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
 
 # Combine the selected columns from matgrp with the group names

diff --git a/tools/camera/CAMERA_groupCorr.R b/tools/camera/CAMERA_groupCorr.R
@@ -23,8 +23,8 @@ args <- list(
   numDigitsMZ = as.numeric(args_vec[10]), # Digits for MZ "customname"
   numDigitsRT = as.numeric(args_vec[11]), # Digits for RT "customname"
   convertRTMinute = as.logical(args_vec[12]), # TRUE - FALSE
-  singlefile_galaxyPath = args_vec[13], # @COMMAND_FILE_LOAD@
-  singlefile_sampleName = args_vec[14] # @COMMAND_FILE_LOAD@
+  singlefile_galaxyPath = args_vec[14], # @COMMAND_FILE_LOAD@
+  singlefile_sampleName = args_vec[16] # @COMMAND_FILE_LOAD@
 )
 
 print("Converted arguments:")
@@ -171,7 +171,7 @@ ncols <- length(colnames(peakList))
 sample_cols <- length(xa@sample) # Number of samples
 
 # Indices for the columns of interest
-main_cols <- 1:(ncols - (3 + sample_cols)) # Main columns before sample columns
+main_cols <- 1:(ncols - (6 + sample_cols)) # Main columns before sample columns
 tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
 
 # Combine the selected columns from matgrp with the group names

diff --git a/tools/camera/CAMERA_groupFWHM.R b/tools/camera/CAMERA_groupFWHM.R
@@ -19,8 +19,8 @@ args <- list(
   convertRTMinute = as.logical(args_vec[5]), # TRUE - FALSE
   numDigitsMZ = as.numeric(args_vec[6]), # Number of digits MZ
   numDigitsRT = as.numeric(args_vec[7]), # Number of digits RT
-  singlefile_galaxyPath = args_vec[8], # @COMMAND_FILE_LOAD@
-  singlefile_sampleName = args_vec[9] # @COMMAND_FILE_LOAD@
+  singlefile_galaxyPath = args_vec[9], # @COMMAND_FILE_LOAD@
+  singlefile_sampleName = args_vec[11] # @COMMAND_FILE_LOAD@
 )
 
 print("Converted arguments:")
@@ -186,7 +186,7 @@ ncols <- length(colnames(peakList))
 sample_cols <- length(xa@sample) # Number of samples
 
 # Indices for the columns of interest
-main_cols <- 1:(ncols - (3 + sample_cols)) # Main columns before sample columns
+main_cols <- 1:(ncols - (6 + sample_cols)) # Main columns before sample columns
 tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
 
 # Combine the selected columns from matgrp with the group names

diff --git a/tools/camera/findAdducts.xml b/tools/camera/findAdducts.xml
@@ -111,7 +111,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="image" value="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData" />
+            <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.fwhm.groupCorr.findIsotopes.RData" />
             <!--<param name="ppm" value="5" />
             <param name="mzabs" value="0.015" />
             <param name="polarity" value="positive" />
@@ -121,8 +121,8 @@
             <param name="max_peaks" value="100" />
             <param name="psg_list" value="NULL" />-->
             <expand macro="test_file_load_single"/>
-            <output name="variableMetadata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv" />
-            <output name="camera_findAdducts_rdata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData" />
+            <output name="variableMetadata" file="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv" />
+            <output name="camera_findAdducts_rdata" file="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData" />
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/camera/findIsotopes.xml b/tools/camera/findIsotopes.xml
@@ -50,7 +50,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="image" value="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData" />
+            <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.fwhm.groupCorr.RData" />
             <!--<param name="maxcharge" value="3" />
             <param name="maxiso" value="4" />
             <param name="ppm" value="5" />
@@ -59,8 +59,8 @@
             <param name="minfrac" value="0.5" />
             <param name="filter" value="FALSE" />-->
             <expand macro="test_file_load_single"/>
-            <output name="variableMetadata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.variableMetadata.tsv" />
-            <output name="camera_findIsotopes_rdata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData" />
+            <output name="variableMetadata" file="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.fwhm.groupCorr.findIsotopes.variableMetadata.tsv" />
+            <output name="camera_findIsotopes_rdata" file="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.fwhm.groupCorr.findIsotopes.RData" />
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/camera/groupCorr.xml b/tools/camera/groupCorr.xml
@@ -58,7 +58,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="image" value="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.RData" />
+            <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.fwhm.RData" />
             <!--<param name="cor_eic_th" value="0.75" />
             <param name="pval" value="0.05" />
             <param name="graphMethod" value="hcs" />
@@ -68,8 +68,8 @@
             <param name="cor_exp_th" value="0.75" />
             <param name="intval" value="into" />-->
             <expand macro="test_file_load_single"/>
-            <output name="variableMetadata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.variableMetadata.tsv" />
-            <output name="camera_groupCorr_rdata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData" />
+            <output name="variableMetadata" file="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.fwhm.groupCorr.variableMetadata.tsv" />
+            <output name="camera_groupCorr_rdata" file="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.fwhm.groupCorr.RData" />
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/camera/groupFWHM.xml b/tools/camera/groupFWHM.xml
@@ -43,13 +43,13 @@
 
     <tests>
         <test>
-            <param name="image" value="xset.merged.groupChromPeaks.fillChromPeaks.RData" />
+            <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.RData" />
             <!--<param name="sigma" value="6" />
             <param name="perfwhm" value="0.6" />
             <param name="intval" value="into" />-->
             <expand macro="test_file_load_single"/>
-            <output name="variableMetadata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.variableMetadata.tsv" />
-            <output name="camera_fwhm" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.rdata" />
+            <output name="variableMetadata" file="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.fwhm.variableMetadata.tsv" />
+            <output name="camera_fwhm" file="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.fwhm.rdata" />
         </test>
     </tests>
     <help><![CDATA[