New tool: FastSpar a tool for correlation estimation for compositional data.#7059
New tool: FastSpar a tool for correlation estimation for compositional data.#7059bgruening merged 8 commits intogalaxyproject:mainfrom
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FastSpar is a C++ implementation of the SparCC algorithm for estimating correlations from compositional data. FastSpar GitHub: https://github.com/scwatts/fastspar The tool wrapper is split into three files: - fastspar: Only perform the correlation and covariance matrix estimation. - fastspar_pvalues: Estimate pvalues for the correlation table. Both steps require some identical parameters, so this tool can also generate correlation and covariance tables. This saves the user from having to copy some parameter values, by only using this tool. - fastspar_reduce: Filter the combined correlations and p-values to generate sparse matrices. The test files are copied or generated from the FastSpar / SparCC repos.
tools/fastspar/fastspar.xml
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| <tool id="fastspar" name="FastSpar" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2"> | |||
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Maybe we should choose a slightly older profile.
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ping ... please also put the profile version into a macro
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I changed the profile to 23.0.
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We should make this a suite. See here
tools-iuc/tools/ampvis2/.shed.yml
Line 11 in 4889f07
…pvalues This removes the help text "Must match the value used in the original FastSpar run.", but this warning is also visible in other places in the tool.
| --correlation '$correlation' | ||
| --covariance '$covariance' | ||
| --threads \${GALAXY_SLOTS:-1} | ||
| --yes |
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can you please add a comment ## what this param is doing?
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This parameter is necessary to skip a continue prompt when an OTU has only one permutation (all samples have identical counts).
The wrapper should probably pass the warning message to the user (beyond the error hidden in the job information panel), but I'm not sure if the problem is severe enough to fail the tool execution.
tools/fastspar/fastspar.xml
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| <tool id="fastspar" name="FastSpar" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2"> | |||
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ping ... please also put the profile version into a macro
Capture the message or throw error instead?
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
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Thanks! |
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FOR CONTRIBUTOR:
I made a pull request for this tool at bgruening/galaxytools#1637 and @bgruening suggested that I also submit the tool here.