Mercurial > repos > galaxyp > cardinal_combine
diff combine.xml @ 6:bb1ac6b47a6c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
| author | galaxyp |
|---|---|
| date | Wed, 25 Mar 2020 07:02:41 -0400 |
| parents | b41107d8fe89 |
| children | 392b2dfd261d |
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--- a/combine.xml Fri Dec 13 13:54:23 2019 -0500 +++ b/combine.xml Wed Mar 25 07:02:41 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="cardinal_combine" name="MSI combine" version="2.2.6.0"> +<tool id="cardinal_combine" name="MSI combine" version="2.2.6.1"> <description> combine several mass spectrometry imaging datasets into one </description> @@ -44,6 +44,7 @@ </command> <configfiles> <configfile name="msi_combine"><![CDATA[ + #import re ################ 1) load libraries and do preparations ################# @@ -86,7 +87,7 @@ #if $infile.ext == 'imzml' #if str($processed_cond.processed_file) == "processed": - msidata_$i <- readImzML('infile_${i}', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE, as = c("MSImageSet")) + msidata_$i <- readImzML('infile_${i}', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE, as = c("MSImageSet")) centroided(msidata_$i) = $centroids #else msidata_$i <- readImzML('infile_${i}', attach.only=TRUE, as = c("MSImageSet")) @@ -235,7 +236,7 @@ #end for -######################### 6a) combination same mz axis ################### +######################### 6b) combination same mz axis ################### #if str( $combine_conditional.combine_method ) == 'automatic_combine': print("automatic combine") @@ -294,12 +295,7 @@ ## save msidata as imzML file MALDIquant MALDIquantForeign::exportImzMl(filtered_dataset, file="out.imzML", processed=TRUE, coordinates=coordinates_matrix) - ## create x,y,sample_name dataframe for QC pdf - ## position_df = unique_coordinates ### ! anders - ## colnames(position_df)[3] = "sample_name" - ##coordinates_combined = coordinates_combined[pixelsofinterest,] ###! anders coordinates_combined = unique_coordinates -##TODO: hier aufräumen kann alles weg?! #end if @@ -323,7 +319,6 @@ guides(fill=guide_legend(ncol=4,byrow=TRUE)) coord_labels = aggregate(cbind(x,y)~sample_name, data=coordinates_combined[,1:3], mean) coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) - print(combine_plot) #if str($annotation_cond.annotation_tabular) == 'annotation' @@ -431,7 +426,7 @@ <output name="pixel_annotations" file="123_annotation_output.tabular"/> <output name="QC_overview" file="123_combined_QC.pdf" compare="sim_size"/> <output name="outfile_imzml" ftype="imzml" file="123_combined.imzml.txt" compare="sim_size"> - <extra_files type="file" file="123_combined.imzml" name="imzml" lines_diff="4"/> + <extra_files type="file" file="123_combined.imzml" name="imzml" lines_diff="12"/> <extra_files type="file" file="123_combined.ibd" name="ibd" compare="sim_size"/> </output> </test> @@ -447,7 +442,7 @@ <output name="pixel_annotations" file="picked.tabular"/> <output name="QC_overview" file="picked_QC.pdf" compare="sim_size"/> <output name="outfile_imzml" ftype="imzml" file="picked.imzml.txt" compare="sim_size"> - <extra_files type="file" file="picked.imzml" name="imzml" lines_diff="6"/> + <extra_files type="file" file="picked.imzml" name="imzml" lines_diff="12"/> <extra_files type="file" file="picked.ibd" name="ibd" compare="sim_size"/> </output> </test> @@ -461,7 +456,7 @@ <output name="QC_overview" file="123_combined_auto.pdf" compare="sim_size"/> <output name="pixel_annotations" file="123_combined_auto.tabular"/> <output name="outfile_imzml" ftype="imzml" file="123_combined_auto.imzml.txt" compare="sim_size"> - <extra_files type="file" file="123_combined_auto.imzml" name="imzml" lines_diff="4"/> + <extra_files type="file" file="123_combined_auto.imzml" name="imzml" lines_diff="12"/> <extra_files type="file" file="123_combined_auto.ibd" name="ibd" compare="sim_size"/> </output> </test> @@ -477,7 +472,7 @@ <output name="pixel_annotations" file="12_annotation_output.tabular"/> <output name="QC_overview" file="12_combined_QC.pdf" compare="sim_size"/> <output name="outfile_imzml" ftype="imzml" file="12_combined.imzml.txt" compare="sim_size"> - <extra_files type="file" file="12_combined.imzml" name="imzml" lines_diff="4"/> + <extra_files type="file" file="12_combined.imzml" name="imzml" lines_diff="12"/> <extra_files type="file" file="12_combined.ibd" name="ibd" compare="sim_size"/> </output> </test> @@ -493,7 +488,7 @@ <output name="pixel_annotations" file="112_annotation_output.tabular"/> <output name="QC_overview" file="112_auto_combined_QC.pdf" compare="sim_size"/> <output name="outfile_imzml" ftype="imzml" file="112_auto_combined.imzml.txt" compare="sim_size"> - <extra_files type="file" file="112_auto_combined.imzml" name="imzml" lines_diff="4"/> + <extra_files type="file" file="112_auto_combined.imzml" name="imzml" lines_diff="12"/> <extra_files type="file" file="112_auto_combined.ibd" name="ibd" compare="sim_size"/> </output> </test> @@ -507,7 +502,7 @@ <output name="pixel_annotations" file="2123_annotation_output.tabular"/> <output name="QC_overview" file="2123_auto_combined_QC.pdf" compare="sim_size"/> <output name="outfile_imzml" ftype="imzml" file="2123_auto_combined.imzml.txt" compare="sim_size"> - <extra_files type="file" file="2123_auto_combined.imzml" name="imzml" lines_diff="4"/> + <extra_files type="file" file="2123_auto_combined.imzml" name="imzml" lines_diff="12"/> <extra_files type="file" file="2123_auto_combined.ibd" name="ibd" compare="sim_size"/> </output> </test> @@ -558,7 +553,7 @@ **Output** -- MSI data as imzML file (in continous format when m/z axis were the same; in processed format when m/z axis were different) +- MSI data as imzML file (in continuous format when m/z axis were the same; in processed format when m/z axis were different) - Pdf with pixel positions and annotations of the combined files - Tabular file with pixel annotations (x,y,column with input file names and annotation columns)