Mercurial > repos > galaxyp > msi_combine
comparison msi_combine.xml @ 7:19d8eee15959 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
author | galaxyp |
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date | Wed, 22 Aug 2018 13:41:16 -0400 |
parents | f4aafc565aa3 |
children | c6564ddf0744 |
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6:f4aafc565aa3 | 7:19d8eee15959 |
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1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.4"> | 1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.5"> |
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 <requirements> | 5 <requirements> |
6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> | 6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> |
7 <requirement type="package" version="2.2.1">r-ggplot2</requirement> | 7 <requirement type="package" version="3.0.0">r-ggplot2</requirement> |
8 </requirements> | 8 </requirements> |
9 <command detect_errors="exit_code"> | 9 <command detect_errors="exit_code"> |
10 <![CDATA[ | 10 <![CDATA[ |
11 #for $i, $infile in enumerate($infiles): | 11 #for $i, $infile in enumerate($infiles): |
12 #if $infile.ext == 'imzml' | 12 #if $infile.ext == 'imzml' |
89 ## read annotation data, up to 5 annotations can be used for now | 89 ## read annotation data, up to 5 annotations can be used for now |
90 | 90 |
91 ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata | 91 ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata |
92 input_annotation = read.delim("annotation_file_${i}.tabular", header = TRUE, | 92 input_annotation = read.delim("annotation_file_${i}.tabular", header = TRUE, |
93 stringsAsFactors = FALSE) | 93 stringsAsFactors = FALSE) |
94 | |
95 if (class(input_annotation[,1]) == "character"){ | |
96 annotation_coordinates = matrix(unlist(strsplit(as.character(input_annotation[,1]), "\\,")), ncol=2, byrow=TRUE) | |
97 annotation_coordinates2 = cbind(as.numeric(substring(annotation_coordinates[,1], 5, last = 1000000L)), as.numeric(substring(annotation_coordinates[,2], 5, last = 1000000L))) | |
98 input_annotation = cbind(annotation_coordinates2, input_annotation[,-1]) | |
99 } | |
100 | |
94 colnames(input_annotation)[1:2] = c("x", "y") | 101 colnames(input_annotation)[1:2] = c("x", "y") |
95 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i)) | 102 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i)) |
96 colnames(msidata_coordinates)[3] = "pixel_index" | 103 colnames(msidata_coordinates)[3] = "pixel_index" |
97 ## only first 5 annotation columns are kept | 104 ## only first 5 annotation columns are kept |
98 if (ncol(input_annotation) > 7){ | 105 if (ncol(input_annotation) > 7){ |
130 #elif str( $combine_conditional.combine_method ) == 'automatic_combine': | 137 #elif str( $combine_conditional.combine_method ) == 'automatic_combine': |
131 names_vector = character() | 138 names_vector = character() |
132 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) ## use name of inputfile from Galaxy | 139 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) ## use name of inputfile from Galaxy |
133 if (sum(spectra(msidata_$i)[],na.rm=TRUE)>0) ## use only valid files | 140 if (sum(spectra(msidata_$i)[],na.rm=TRUE)>0) ## use only valid files |
134 { | 141 { |
135 if (is.null(levels(msidata_$i\$combined_sample))) ### if the file was not combined before use input file name, otherwise keep combined_sample name which was assigned before | 142 if (is.null(levels(msidata_$i\$combined_sample))) |
136 { | 143 { |
137 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i))) | 144 names_vector = append(names_vector, rep(paste($i+1, "$escaped_element_identifier", sep="_"),ncol(msidata_$i))) |
138 msidata_$i\$combined_sample = as.factor(names_vector) | 145 msidata_$i\$combined_sample = as.factor(names_vector) |
139 } | 146 } |
140 } | 147 } |
400 <option value="ppm" selected="True" >ppm</option> | 407 <option value="ppm" selected="True" >ppm</option> |
401 </param> | 408 </param> |
402 </when> | 409 </when> |
403 </conditional> | 410 </conditional> |
404 <param name="annotation_files" type="data" multiple="true" format="tabular" | 411 <param name="annotation_files" type="data" multiple="true" format="tabular" |
405 label="Pixel annotations as tabular files" | 412 label="Pixel annotations as tabular files, same number and order of files as input files" |
406 help="Tabular files should have the same order as input files"/> | 413 help="Coordinates in column 1 in format x = 1, y = 1 or first column x values, second column y values. Up to 5 columns with pixel annotations"/> |
407 <conditional name="combine_conditional"> | 414 <conditional name="combine_conditional"> |
408 <param name="combine_method" type="select" label="Select the way you want to combine multiple files" help="More detailed help can be found in the help section at the bottom"> | 415 <param name="combine_method" type="select" label="Select the way you want to combine multiple files" help="More detailed help can be found in the help section at the bottom"> |
409 <option value="automatic_combine" selected="True" >automatic combination</option> | 416 <option value="automatic_combine" selected="True" >automatic combination</option> |
410 <option value="xy_shifts">shift xy coordinates with a tabular file</option> | 417 <option value="xy_shifts">shift xy coordinates with a tabular file</option> |
411 </param> | 418 </param> |
439 <param name="column_names" value="3"/> | 446 <param name="column_names" value="3"/> |
440 <param name="output_matrix" value="True"/> | 447 <param name="output_matrix" value="True"/> |
441 <output name="matrixasoutput" file="123_combined_matrix.tabular"/> | 448 <output name="matrixasoutput" file="123_combined_matrix.tabular"/> |
442 <output name="annotation_output" file="123_annotation_output.tabular"/> | 449 <output name="annotation_output" file="123_annotation_output.tabular"/> |
443 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" /> | 450 <output name="msidata_combined" file="123_combined.RData" compare="sim_size" /> |
444 <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="20000"/> | 451 <output name="combining_qc" file="123_combined_QC.pdf" compare="sim_size" delta="2000"/> |
445 </test> | 452 </test> |
446 <test expect_num_outputs="4"> | 453 <test expect_num_outputs="4"> |
447 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/> | 454 <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/> |
448 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/> | 455 <param name="annotation_files" value="annotations_file1.tabular,annotations_file2.tabular" ftype="tabular"/> |
449 <param name="combine_method" value="automatic_combine"/> | 456 <param name="combine_method" value="automatic_combine"/> |
450 <param name="output_matrix" value="True"/> | 457 <param name="output_matrix" value="True"/> |
451 <output name="matrixasoutput" file="12_combined_matrix.tabular"/> | 458 <output name="matrixasoutput" file="12_combined_matrix.tabular"/> |
452 <output name="annotation_output" file="12_annotation_output.tabular"/> | 459 <output name="annotation_output" file="12_annotation_output.tabular"/> |
453 <output name="msidata_combined" file="12_combined.RData" compare="sim_size" /> | 460 <output name="msidata_combined" file="12_combined.RData" compare="sim_size" /> |
454 <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="20000"/> | 461 <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="2000"/> |
455 </test> | 462 </test> |
456 <test expect_num_outputs="3"> | 463 <test expect_num_outputs="3"> |
457 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/> | 464 <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/> |
458 <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/> | 465 <param name="annotation_files" value="annotations_file1.tabular,123_annotation.tabular" ftype="tabular"/> |
459 <param name="combine_method" value="automatic_combine"/> | 466 <param name="combine_method" value="automatic_combine"/> |
460 <param name="output_matrix" value="False"/> | 467 <param name="output_matrix" value="False"/> |
461 <output name="annotation_output" file="112_annotation_output.tabular"/> | 468 <output name="annotation_output" file="112_annotation_output.tabular"/> |
462 <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" /> | 469 <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" /> |
463 <output name="combining_qc" file="112_auto_combined_QC.pdf" compare="sim_size" delta="20000"/> | 470 <output name="combining_qc" file="112_auto_combined_QC.pdf" compare="sim_size" delta="2000"/> |
464 </test> | 471 </test> |
465 </tests> | 472 </tests> |
466 <help> | 473 <help> |
467 <![CDATA[ | 474 <![CDATA[ |
468 | 475 |