| Previous changeset 7:5e6f8fb2df07 (2020-04-23) Next changeset 9:08ebd8da780c (2020-09-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2" |
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modified:
macros.xml test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.imzml.txt test-data/preprocessing_results1.pdf test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.imzml.txt test-data/preprocessing_results2.pdf test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzml test-data/preprocessing_results3.imzml.txt test-data/preprocessing_results3.pdf test-data/preprocessing_results4.ibd test-data/preprocessing_results4.imzml test-data/preprocessing_results4.imzml.txt test-data/preprocessing_results4.pdf test-data/preprocessing_results5.ibd test-data/preprocessing_results5.imzml test-data/preprocessing_results5.imzml.txt test-data/preprocessing_results5.pdf |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 macros.xml --- a/macros.xml Thu Apr 23 08:08:28 2020 -0400 +++ b/macros.xml Wed May 13 14:27:51 2020 -0400 |
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| @@ -32,6 +32,12 @@ <token name="@READING_MSIDATA@"><![CDATA[ ## importing MSI data files + ## read RData files (MSI and other data) independent of filename + loadRData <- function(fileName){ + load(fileName) + get(ls()[ls() != "fileName"]) + } + #if $infile.ext == 'imzml' #if str($processed_cond.processed_file) == "processed": msidata <- readImzML('infile', resolution=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units") @@ -45,11 +51,6 @@ msidata = readAnalyze('infile', attach.only=TRUE) centroided(msidata) = $centroids #else - ## function to read RData files independent of filename - loadRData <- function(fileName){ - load(fileName) - get(ls()[ls() != "fileName"]) - } msidata = loadRData('infile.RData') #end if |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/QC_analyze75.pdf |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/QC_imzml.pdf |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/QC_rdata.pdf |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results1.ibd |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Thu Apr 23 08:08:28 2020 -0400 +++ b/test-data/preprocessing_results1.imzml Wed May 13 14:27:51 2020 -0400 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="722d404b-4188-40b4-a3b2-3764ebbdecad" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c5aded0bab57fd7317901ff7709f2395fc91152e" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="25fb4349-d529-4b12-8523-a6aa0306ecf4" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7f41f9f5efcb31248caefc91b7d6edce87d7f42c" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results1.imzml.txt --- a/test-data/preprocessing_results1.imzml.txt Thu Apr 23 08:08:28 2020 -0400 +++ b/test-data/preprocessing_results1.imzml.txt Wed May 13 14:27:51 2020 -0400 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 216 Mär 24 10:39 ibd --rw-r--r-- 1 meli meli 18090 Mär 24 10:39 imzml +-rw-r--r-- 1 meli meli 216 Mai 10 17:37 ibd +-rw-r--r-- 1 meli meli 18090 Mai 10 17:37 imzml |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results1.pdf |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results2.ibd |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results2.imzml --- a/test-data/preprocessing_results2.imzml Thu Apr 23 08:08:28 2020 -0400 +++ b/test-data/preprocessing_results2.imzml Wed May 13 14:27:51 2020 -0400 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="e536d1e2-427b-4c5b-9743-8210ae52a564" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7cea783e9d345946b874fc1f25d40ce90bffd2f9" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="fa59b434-12e0-47fe-b338-814c92daa7d6" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5764be27b51a23d8c23e4c93befb9d8e57161bd9" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results2.imzml.txt --- a/test-data/preprocessing_results2.imzml.txt Thu Apr 23 08:08:28 2020 -0400 +++ b/test-data/preprocessing_results2.imzml.txt Wed May 13 14:27:51 2020 -0400 |
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| @@ -1,4 +1,4 @@ imzML file: total 64 --rw-r--r-- 1 meli meli 37404 Mär 24 10:40 ibd --rw-r--r-- 1 meli meli 22796 Mär 24 10:40 imzml +-rw-r--r-- 1 meli meli 37404 Mai 10 17:38 ibd +-rw-r--r-- 1 meli meli 22796 Mai 10 17:38 imzml |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results2.pdf |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results3.ibd |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results3.imzml --- a/test-data/preprocessing_results3.imzml Thu Apr 23 08:08:28 2020 -0400 +++ b/test-data/preprocessing_results3.imzml Wed May 13 14:27:51 2020 -0400 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="df9dd256-6485-4954-8338-ddb0c760d4dc" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ea9ad44f2615ef4d24b92d3ceb38dfa8ec47a978" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="d11b7693-3397-4d1f-9e67-29d952701100" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="94906879d47bbdcf97126d50c906dfd76e6681e4" /> <cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" /> </fileContent> </fileDescription> |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results3.imzml.txt --- a/test-data/preprocessing_results3.imzml.txt Thu Apr 23 08:08:28 2020 -0400 +++ b/test-data/preprocessing_results3.imzml.txt Wed May 13 14:27:51 2020 -0400 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 960 Apr 22 15:36 ibd --rw-r--r-- 1 meli meli 18112 Apr 22 15:36 imzml +-rw-r--r-- 1 meli meli 960 Mai 10 17:39 ibd +-rw-r--r-- 1 meli meli 18112 Mai 10 17:39 imzml |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results4.imzml --- a/test-data/preprocessing_results4.imzml Thu Apr 23 08:08:28 2020 -0400 +++ b/test-data/preprocessing_results4.imzml Wed May 13 14:27:51 2020 -0400 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="db79298c-8368-42d7-84fc-18cad6ef1924" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="18bae3cc87b4c9aab2577cffe2fbc7425a93270b" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c6122884-ceb5-46b6-9160-5d28e8862946" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="03e4b58b8e63517605164e90b85fe93a851a9c5b" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results4.imzml.txt --- a/test-data/preprocessing_results4.imzml.txt Thu Apr 23 08:08:28 2020 -0400 +++ b/test-data/preprocessing_results4.imzml.txt Wed May 13 14:27:51 2020 -0400 |
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| @@ -1,4 +1,4 @@ imzML file: total 84 --rw-r--r-- 1 meli meli 63256 Mär 24 11:35 ibd --rw-r--r-- 1 meli meli 18199 Mär 24 11:35 imzml +-rw-r--r-- 1 meli meli 63256 Mai 10 17:40 ibd +-rw-r--r-- 1 meli meli 18199 Mai 10 17:40 imzml |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results5.imzml --- a/test-data/preprocessing_results5.imzml Thu Apr 23 08:08:28 2020 -0400 +++ b/test-data/preprocessing_results5.imzml Wed May 13 14:27:51 2020 -0400 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="1cb5b7df-bc82-4588-9a14-1dd58a3983a7" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="a16bf7a9d9d4064ce94821e3e7df2681725a497b" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="3aff713c-00ec-422d-b63d-efd45fbdd7cc" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9316138c1e7484662943bb206c79c2d074121530" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r 5e6f8fb2df07 -r a69865da6f80 test-data/preprocessing_results5.imzml.txt --- a/test-data/preprocessing_results5.imzml.txt Thu Apr 23 08:08:28 2020 -0400 +++ b/test-data/preprocessing_results5.imzml.txt Wed May 13 14:27:51 2020 -0400 |
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| @@ -1,4 +1,4 @@ imzML file: total 428 --rw-r--r-- 1 meli meli 415936 Apr 19 21:07 ibd --rw-r--r-- 1 meli meli 18569 Apr 19 21:07 imzml +-rw-r--r-- 1 meli meli 415936 Mai 10 17:40 ibd +-rw-r--r-- 1 meli meli 18569 Mai 10 17:40 imzml |
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