| Previous changeset 0:a2988d8d4b77 (2018-10-01) Next changeset 2:0c4579390f73 (2019-02-15) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c |
|
modified:
filtering.xml macros.xml test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_rdata.pdf test-data/Plot_analyze75.pdf test-data/Plot_analyze75_allpixels.pdf test-data/Plot_empty_spectra.pdf test-data/Plot_imzml.pdf test-data/Plot_rdata.pdf test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/analyze75.svg test-data/analyze75_filtered2.pdf test-data/analyze_filteredoutside.RData test-data/centroids_rdata.pdf test-data/cluster_skm.RData test-data/imzml_filtered3.RData test-data/imzml_filtered3.pdf test-data/imzml_filtered4.RData test-data/imzml_filtered4.pdf test-data/imzml_filtered5.RData test-data/imzml_filtered5.pdf test-data/kmeans_analyze.pdf test-data/pca_imzml.pdf test-data/rdata_notfiltered.RData test-data/rdata_notfiltered.pdf test-data/test1.pdf test-data/test2.pdf test-data/test2.rdata test-data/test3.pdf test-data/test4.pdf test-data/test4.rdata test-data/test5.pdf test-data/test6.pdf test-data/test6.rdata test-data/test7.pdf test-data/test7.rdata |
|
removed:
test-data/imzml_filtered2.RData test-data/imzml_filtered2.pdf |
| b |
| diff -r a2988d8d4b77 -r aac805a9d2ae filtering.xml --- a/filtering.xml Mon Oct 01 01:04:17 2018 -0400 +++ b/filtering.xml Thu Oct 25 07:25:13 2018 -0400 |
| [ |
| b'@@ -1,21 +1,34 @@\n-<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.0">\n+<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.1">\n <description>tool for filtering mass spectrometry imaging data</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements">\n- <requirement type="package" version="2.2.1">r-gridextra</requirement>\n- <requirement type="package" version="2.2.1">r-ggplot2</requirement>\n+ <requirement type="package" version="2.3">r-gridextra</requirement>\n+ <requirement type="package" version="3.0">r-ggplot2</requirement>\n </expand>\n+ <expand macro="print_version"/>\n <command detect_errors="exit_code">\n <![CDATA[\n \n @INPUT_LINKING@\n cat \'${MSI_subsetting}\' &&\n- Rscript \'${MSI_subsetting}\'\n+ Rscript \'${MSI_subsetting}\' &&\n+\n+ #if $imzml_output:\n+ mkdir $outfile_imzml.files_path &&\n+ ls -l &&\n+ mv ./out.imzML "${os.path.join($outfile_imzml.files_path, \'imzml\')}" | true &&\n+ mv ./out.ibd "${os.path.join($outfile_imzml.files_path, \'ibd\')}" | true &&\n+ #end if\n+ echo "imzML file:" > $outfile_imzml &&\n+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml\n+\n \n ]]>\n </command>\n+\n+\n <configfiles>\n <configfile name="MSI_subsetting"><![CDATA[\n \n@@ -112,8 +125,9 @@\n msidata = msidata[, coord(msidata)\\$x <= $pixels_cond.max_x_range & coord(msidata)\\$x >= $pixels_cond.min_x_range]\n msidata = msidata[, coord(msidata)\\$y <= $pixels_cond.max_y_range & coord(msidata)\\$y >= $pixels_cond.min_y_range]\n }else{\n- msidata = msidata[,0]\n- print("no valid pixel found")}\n+\n+ print("no valid pixel found")\n+ msidata = msidata[,0]}\n \n ## update position_df for filtered pixels\n position_df = cbind(coord(msidata)[,1:2], rep("$infile.element_identifier", times=ncol(msidata)))\n@@ -138,103 +152,121 @@\n ####################### Keep m/z from tabular file #########################\n \n ## feature filtering only when pixels/features/intensities are left\n+\n+if (ncol(msidata) > 0){\n npeaks_before_filtering= sum(spectra(msidata)[]>0, na.rm=TRUE)\n+ if (npeaks_before_filtering > 0)\n+ {\n+\n+ #if str($features_cond.features_filtering) == "features_list":\n+ print("feature list")\n+\n+ ## read tabular file, define starting row, extract and count valid features\n+ input_features = read.delim("$mz_tabular", header = $features_cond.feature_header, stringsAsFactors = FALSE)\n+ extracted_features = input_features[,$features_cond.feature_column]\n+ numberfeatures = length(extracted_features)\n+ if (class(extracted_features) == "numeric"){\n+ ### max digits given in the input file will be used to match m/z but the maximum is 4\n+ max_digits = max(nchar(sapply(strsplit(as.character(extracted_features), "\\\\."),`[`,2)), na.rm=TRUE)\n+\n+ if (max_digits >4)\n+ {\n+ max_digits = 4\n+ }\n+\n+ validfeatures = round(extracted_features, max_digits) %in% round(mz(msidata),max_digits)\n+ featuresofinterest = features(msidata)[round(mz(msidata), digits = max_digits) %in% round(extracted_features[validfeatures], max_digits)]\n+ validmz = length(unique(featuresofinterest))\n+ }else{\n+ validmz = 0\n+ featuresofinterest = 0}\n+\n+ ### filter msidata for valid features\n+ msidata = msidata[featuresofinterest,]\n+\n+ ############### features within a given range are kept #####################\n+\n+ #elif str($features_cond.features_filtering) == "features_range":\n+ print("feature range")\n+\n+ numberfeatures = "range"\n+ validm'..b'an" label="Output of imzML file" truevalue="TRUE" falsevalue="FALSE"/>\n+\n </inputs>\n \n <outputs>\n <data format="rdata" name="msidata_filtered" label="${tool.name} on ${on_string}"/>\n <data format="pdf" name="QC_overview" from_work_dir="filtertool_QC.pdf" label = "${tool.name} on ${on_string}: QC"/>\n+ <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML">\n+ <filter>imzml_output</filter>\n+ </data>\n </outputs>\n <tests>\n <test>\n <expand macro="infile_imzml"/>\n <param name="pixel_filtering" value="pixel_range"/>\n- <param name="min_x_range" value="10"/>\n- <param name="max_x_range" value="20"/>\n- <param name="min_y_range" value="2"/>\n- <param name="max_y_range" value="2"/>\n- <output name="QC_overview" file="imzml_filtered2.pdf" compare="sim_size"/>\n- <output name="msidata_filtered" file="imzml_filtered2.RData" compare="sim_size"/>\n- </test>\n- <test>\n- <expand macro="infile_imzml"/>\n- <param name="pixel_filtering" value="pixel_range"/>\n <param name="min_x_range" value="1"/>\n <param name="max_x_range" value="20"/>\n <param name="min_y_range" value="2"/>\n@@ -447,6 +469,10 @@\n <param name="column_names" value="2"/>\n <output name="QC_overview" file="imzml_filtered4.pdf" compare="sim_size"/>\n <output name="msidata_filtered" file="imzml_filtered4.RData" compare="sim_size"/>\n+ <!--imzml output test not yet working: output name="outfile_imzml" file="filtering_imzmls/summary" compare="sim_size" delta="10000">\n+ <extra_files type="file" name="imzml" value="filtering_imzmls/out4.imzML" compare="sim_size" delta="10000"/>\n+ <extra_files type="file" name="ibd" value="filtering_imzmls/out4.ibd" compare="sim_size" delta="10000"/>\n+ </output-->\n </test>\n <test>\n <expand macro="infile_imzml"/>\n@@ -493,8 +519,8 @@\n \n **Options**\n \n-- pixel filtering/annotation: either with a tabular file containing x and y coordinates and pixel annotations or by defining a range for x and y by hand (for the latter no annotation is possible). Pixel that are not present in the dataset are ignored. In case all pixels are not present in the dataset the output file will be empty and no further mz filtering will be performed. \n-- m/z feature filtering: m/z values for filtering should be either imported as a tabular file containing containing m/z of interest or by defining a range for the m/z values. m/z that are not present in the dataset are ignored. If all given m/z values or the m/z range is outside the dataset, the output file will be empty. \n+- pixel filtering/annotation: either with a tabular file containing x and y coordinates and pixel annotations or by defining a range for x and y by hand (for the latter no annotation is possible). Pixel that are not present in the dataset are ignored. It is not possible to filter only for pixels that are not present in the dataset. \n+- m/z feature filtering: m/z values for filtering should be either imported as a tabular file containing containing m/z of interest or by defining a range for the m/z values. m/z that are not present in the dataset are ignored. It is not possible to filter only for m/z that are not present in the dataset. \n - m/z feature removing: perturbing m/z features such as matrix contaminants can be removed by specifying their m/z in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed.\n \n \n@@ -506,7 +532,8 @@\n \n **Output**\n \n-- imzML file filtered for pixels and/or m/z\n+- MSI data as .RData output (can be read with the Cardinal package in R)\n+- optional: MSI data as imzML file\n - pdf with heatmap showing the pixels that are left after filtering and histograms of kept and removed m/z\n \n \n' |
| b |
| diff -r a2988d8d4b77 -r aac805a9d2ae macros.xml --- a/macros.xml Mon Oct 01 01:04:17 2018 -0400 +++ b/macros.xml Thu Oct 25 07:25:13 2018 -0400 |
| [ |
| @@ -4,10 +4,17 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement> + <requirement type="package" version="3.5.1">r-base</requirement> <yield/> </requirements> </xml> + <xml name="print_version"> + <version_command><![CDATA[ +echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\$otherPkgs\$Cardinal\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + </xml> + <token name="@INPUT_LINKING@"><