Mercurial > repos > galaxyp > cardinal_combine

comparison combine.xml @ 14:5f066029763e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7-dirty"
author galaxyp
date Fri, 19 Feb 2021 18:54:56 +0000
parents 7e18fcb92a6a
children aad328eb6c0f
comparison
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13:e215f71d7983 14:5f066029763e
1 <tool id="cardinal_combine" name="MSI combine" version="@VERSION@.0"> 1 <tool id="cardinal_combine" name="MSI combine" version="@VERSION@.1">
2 <description> 2 <description>
3 combine several mass spectrometry imaging datasets into one 3 combine several mass spectrometry imaging datasets into one
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
117 print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file")) 117 print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file"))
118 msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))] 118 msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))]
119 119
120 ## same name for MSI data files necessary to combine data into one single coordinate system 120 ## same name for MSI data files necessary to combine data into one single coordinate system
121 run(msidata_$i) = "msidata" 121 run(msidata_$i) = "msidata"
122
123 ## remove z dimension and 3D information in pixelData to allow combining datasets with and without z dimension
124 coord(msidata_${i})\$z <- NULL
125 pData(msidata_${i})\$'3DPositionX' <- NULL
126 pData(msidata_${i})\$'3DPositionY' <- NULL
122 127
123 ############ 3) Read and process annotation tabular files ###################### 128 ############ 3) Read and process annotation tabular files ######################
124 129
125 #if str($annotation_cond.annotation_tabular) == 'annotation' 130 #if str($annotation_cond.annotation_tabular) == 'annotation'
126 print("annotations") 131 print("annotations")