Mercurial > repos > galaxyp > cardinal_mz_images

comparison mz_images.xml @ 1:4d5f798a7a18 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
author galaxyp
date Thu, 25 Oct 2018 07:27:54 -0400
parents 2ba12c97f7cc
children 27a4c660bbca
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0:2ba12c97f7cc 1:4d5f798a7a18
1 <tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.0"> 1 <tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.1">
2 <description> 2 <description>
3 mass spectrometry imaging m/z heatmaps 3 mass spectrometry imaging m/z heatmaps
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements"> 8 <expand macro="requirements">
9 <requirement type="package" version="2.2.1">r-gridextra</requirement> 9 <requirement type="package" version="2.3">r-gridextra</requirement>
10 <requirement type="package" version="0.20-35">r-lattice</requirement> 10 <requirement type="package" version="0.20_35">r-lattice</requirement>
11 </expand> 11 </expand>
12 <command detect_errors="aggressive"> 12 <command detect_errors="aggressive">
13 <![CDATA[ 13 <![CDATA[
14 @INPUT_LINKING@ 14 @INPUT_LINKING@
15 cat '${MSI_heatmaps}' && 15 cat '${MSI_heatmaps}' &&
48 #if not $filename: 48 #if not $filename:
49 #set $filename = $infile.display_name 49 #set $filename = $infile.display_name
50 #end if 50 #end if
51 title(main=paste("\nHeatmap images\n\n", "Filename:\n", "$filename")) 51 title(main=paste("\nHeatmap images\n\n", "Filename:\n", "$filename"))
52 52
53 new_row = data.frame(paste0(length(inputmz), "/", length(input_list[,1])), paste0("# valid m/z in \n", "$calibrant_file.display_name")) 53 new_row = data.frame(paste0("# valid m/z in \n", "$calibrant_file.display_name"), paste0(length(inputmz), "/", length(input_list[,1])))
54 colnames(new_row) = c("properties", "values") 54 colnames(new_row) = c("properties", "values")
55 property_df = rbind(property_df, new_row) 55 property_df = rbind(property_df, new_row)
56 56
57 grid.table(property_df, rows= NULL) 57 grid.table(property_df, rows= NULL)
58 58