Metams #275
Metams #275
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C'est un peu trompeur sur la marchandise tout ce vert :P Mais pas de soucis pour y travailler avec toi.
Update README.md
Dev planemo conda
add gg format for RI file add txt format for msp file
Add Metabolomics tag in Galaxy toolshed descriptions.
from ticket otrs 2016083010000283 if no peaks in a samples then plotUnknown break
avoid empty dataMatrix when file names contains space or start with numbers
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It would be awesome to have as small test data as we can. I knows its time consuming, but its worth the effort IMHO. git repos can not be that big and we run tests very often. E.g. on IUC we run all tests of all tools with every Galaxy release, which we could also do here. That all said, we do have official support nowadays to specify a URL to a test file, so files can be larger if necessary. |
tools/metams/macros/macros.xml
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tools/metams/macros/macros.xml
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| <xml name="stdio"> | |
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| <exit_code range="1" level="fatal" /> | |
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tools/metams/macros/macros.xml
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| **Please cites** | ||
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| metaMS : Wehrens, R.; Weingart, G.; Mattivi, F. Journal of Chromatography B. | ||
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| xcms : Smith, C. A.; Want, E. J.; O’Maille, G.; Abagyan, R.; Siuzdak, G. Anal. Chem. 2006, 78, 779–787. | ||
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| CAMERA : Kuhl, C.; Tautenhahn, R.; Böttcher, C.; Larson, T. R.; Neumann, S. Analytical Chemistry 2012, 84, 283–289. |
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| **Please cites** | |
| metaMS : Wehrens, R.; Weingart, G.; Mattivi, F. Journal of Chromatography B. | |
| xcms : Smith, C. A.; Want, E. J.; O’Maille, G.; Abagyan, R.; Siuzdak, G. Anal. Chem. 2006, 78, 779–787. | |
| CAMERA : Kuhl, C.; Tautenhahn, R.; Böttcher, C.; Larson, T. R.; Neumann, S. Analytical Chemistry 2012, 84, 283–289. | |
| **Please cites** | |
| metaMS : Wehrens, R.; Weingart, G.; Mattivi, F. Journal of Chromatography B. | |
| xcms : Smith, C. A.; Want, E. J.; O’Maille, G.; Abagyan, R.; Siuzdak, G. Anal. Chem. 2006, 78, 779–787. | |
| CAMERA : Kuhl, C.; Tautenhahn, R.; Böttcher, C.; Larson, T. R.; Neumann, S. Analytical Chemistry 2012, 84, 283–289. |
Is this still needed? We have the proper annotation already.
tools/metams/macros/macros.xml
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| .. class:: infomark | ||
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| **Galaxy wrapper and scripts developpers** Guitton Yann LABERCA [email protected] and Saint-Vanne Julien [email protected] |
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please use the new fancy https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-creator talk
tools/metams/macros/macros.xml
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| </xml> | ||
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| <!-- COMMAND --> | ||
| <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token> |
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We need to quote this path
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| <tool id="metams_runGC" name="metaMS.runGC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> | |||
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| <tool id="metams_runGC" name="metaMS.runGC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> | |
| <tool id="metams_runGC" name="metaMS.runGC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> |
| </macros> | ||
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| <expand macro="requirements"/> | ||
| <expand macro="stdio"/> |
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| <expand macro="stdio"/> |
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instead add the detect_errors tag into the command, like below
| <expand macro="requirements"/> | ||
| <expand macro="stdio"/> | ||
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| <command><
How can this actually be specified? Is there a tutorial for this? This would also be greatly helpful for our tools. |
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https://docs.galaxyproject.org/en/master/dev/schema.html#tool-tests-test-param |
Amazing, thanks! |
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To indent the code in the R files to validate the lintr step, I used the "styler" library from RStudio. The code formatting worked well. |
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Thanks for the efforts. styler is great. Recent versions of the CI also use it instead of / in addition to lintr: https://github.com/galaxyproject/tools-iuc/tree/main/.github (I will try to update CI here).
Two more small comments included.
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This way of defining a suite is outdated. Use suite and auto_tool_repositories in shed.yaml like here https://github.com/galaxyproject/tools-iuc/blob/1019bf0fda897582e2bbdc773aebb3e08e285aae/tools/ampvis2/.shed.yml#L14
If there are different owners this might be a solution: https://github.com/galaxyproject/tools-iuc/blob/main/tool_collections/samtools/.shed.yml
| <param name="EIC" value="true"/> | ||
| <param name="unkn" value="1:5"/> | ||
| </conditional> | ||
| <output name="unknownPdf" value="GCMS_EIC_noDB.pdf" ftype="pdf" compare="sim_size" delta="1200"/> |
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Instead of sim_size you could use a <has_size size="xyz" delta="1200"/> content assertion. Then we do not need to save the actual file in the repo.
Input staging problem: Test input file (alg2.mzData) cannot be found.
| </required_files> | ||
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| <command detect_errors="exit_code"><![CDATA[ | ||
| @COMMAND_RSCRIPT@/metams_plot.r |
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The $__tool_directory__/metams_plot.r should be single quoted.
| <option value="true">YES</option> | ||
| </param> | ||
| <when value="true"> | ||
| <param name="unkn" type="text" value="1:5" label="EIC_Unknown" help="vector of peaks number to be plotted, for example 1:5 (mean 1 to 5) or 1,4,12 (means 1 4 and 12). For all EIC use 0" /> |
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Ideally this would have a validator checking for correct user input.
| </data> | ||
| <!-- Only when user selected EIC option --> | ||
| <data name="unknownPdf" format="pdf" from_work_dir="GCMS_EIC.pdf" label="GCMS_EIC.pdf"> | ||
| <filter>selectedeic['EIC'] is True</filter> |
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Probably selectedeic['EIC'] == "true"
| <data name="variableMetadata" format="tabular" from_work_dir="variableMetadata.tsv" label="variableMetadata.tsv" /> | ||
| <data name="dataMatrix" format="tabular" from_work_dir="dataMatrix.tsv" label="dataMatrix.tsv" /> | ||
| <data name="peakspectra" format="txt" from_work_dir="peakspectra.msp" label="peakspectra.msp" /> | ||
| <data name="rungcRData" format="rdata" from_work_dir="runGC.RData" label="runGC.RData" /> |
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It might be preferable to use format="rds" for the output. In the R-script you might just switch to saveRDS and readRDS. But since you explicitly list the stored objects in the save call also Rdata might be acceptable. Some people have security concerns with rdata.
https://www.matheusmello.io/posts/r-what-are-the-main-differences-between-r-data-files
tools/metams/metams_plot.xml
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| <output name="bpcsRawPdf" value="BPCs_raw.pdf" ftype="pdf" compare="sim_size" delta="2000"/> | ||
| </test> | ||
| <!-- Test EICs --> | ||
| <test expect_num_outputs="5"> |
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I don't understand how you get to 5 outputs here.
| <param name="metaMS" value="runGC_test.RData" ftype="rdata" /> | ||
| <expand macro="test_file_load_alg_symlink" /> | ||
| <param name="selectedtic" value="true"/> | ||
| <output name="ticsRawPdf" value="TICs_raw.pdf" ftype="pdf" compare="sim_size" delta="600"/> |
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Instead of saving the file for comparison and having a sim_size comparison we could use https://docs.galaxyproject.org/en/master/dev/schema.html#has-size with equivalent results
| <option value="hide" selected="true">hide</option> | ||
| </param> | ||
| <when value="show"> | ||
| <param name="rtrange" type="text" value="" label="RTrange" help="RT range to process in minutes, for example 5,25" > |
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Also here an additional validator might be helpful.
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rt_range appears again below. Could be a macro
| <option value="hide" selected="true">hide</option> | ||
| </param> | ||
| <when value="show"> | ||
| <param name="db_input" type="data" format="msp,txt" label=" DB file" help="A database file as needed for DB option in runGC" /> |
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What would be the txt input? Could be documented.
This MR merge the metams repository https://github.com/workflow4metabolomics/metaMS/tree/prep_migration in this main one.