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Cameron Hyde
1039c32b72
------ iSEE is a new interactive tool for visualizing single-cell RNAseq data. It requires a new datatype ``rdata.se`` which allows users to upload an R HDF5SummarizedExperiment object.
136 lines
3.6 KiB
XML
136 lines
3.6 KiB
XML
<tool id="interactive_tool_isee" tool_type="interactive" name="iSEE" version="1.0.0">
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<requirements>
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<container type="docker">biocontainers/isee-galaxy:v3.13_cv1.0.0</container>
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</requirements>
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<entry_points>
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<entry_point name="iSEE Single Cell Visualisation" requires_domain="True">
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<!-- This port is exposed by the docker container -->
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<port>8888</port>
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</entry_point>
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</entry_points>
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<command><![CDATA[
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## Container wdir: /import
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#set INPUT_PATH = "sce"
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#set RSCRIPT = '/scripts/isee.R'
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ln -s '$input.extra_files_path' '$INPUT_PATH' &&
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ln -s '$isee_script' '$RSCRIPT' &&
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cp '$isee_script' '$outfile' &&
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## Redirect stderr - unfortunately necessary to stop R "warning" messages from
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## inferring job status as "failed"
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/scripts/run.sh '$RSCRIPT'
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]]>
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</command>
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<configfiles>
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<configfile name="isee_script"><![CDATA[
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## Import render function to template R Shiny app code
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## -----------------------------------------------------------------------------
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#import os
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#import importlib.util
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#set modpath = $os.path.join($__tool_directory__, "isee/render.py")
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#set spec = $importlib.util.spec_from_file_location("render", $modpath)
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#set render = $importlib.util.module_from_spec(spec)
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#$spec.loader.exec_module(render)
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## Stop warning messages being emitted from R while still allowing genuine job failure
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## -----------------------------------------------------------------------------
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devNull <- file("/dev/null", open = "wt")
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sink(devNull, type = "message")
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## Begin R script
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## -----------------------------------------------------------------------------
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library(iSEE)
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library(HDF5Array)
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sce_path <- 'sce'
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sce <- loadHDF5SummarizedExperiment(sce_path)
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$render.app()
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shiny::runApp(app, host="0.0.0.0", port=8888, quiet=TRUE, launch.browser=FALSE)
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]]></configfile>
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</configfiles>
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<inputs>
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<param
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name="input"
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type="data"
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format="rdata.se"
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label="HDF5SummarizedExperiment: rdata.se (composite)"
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help="This datatype represents a HDF5SummarizedExperiment object as
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exported from R."
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/>
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</inputs>
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<outputs>
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<data name="outfile" format="txt"
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label="${tool.name} on ${on_string}: Rscript" />
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</outputs>
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<tests>
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<test expect_num_outputs="1">
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</test>
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</tests>
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<help><![CDATA[
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**Overview**
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iSEE provides a web interface for visualising single-cell transcriptomic
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datasets encapsulated as an HDF5SummarizedExperiment object.
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Full documentation: https://isee.github.io/iSEE/
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-----
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**Input**
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The tool takes a single HDF5SummarizedExperiment object as an input,
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which can be uploaded with the composite datatype ``rdata.se``. This requires
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two input files: ``se.rds`` and ``assays.h5``. Within R, an
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``HDF5SummarizedExperiment`` object can be exported as a directory containing
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these two input files with the function ``saveHDF5SummarizedExperiment()``
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- this will create a folder containing the two files required above.
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These utilities can be installed and imported within R from the ``HDF5Array``
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package.
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-----
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**Useful links:**
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- Documentation on ``HDF5SummarizedExperiment`` data object:
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https://rdrr.io/bioc/HDF5Array/man/saveHDF5SummarizedExperiment.html
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- HDF5Array manual:
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https://bioc.ism.ac.jp/packages/3.7/bioc/manuals/HDF5Array/man/HDF5Array.pdf
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]]></help>
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<citations>
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<citation type="bibtex">
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@article{rue2018isee,
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title={iSEE: interactive summarizedexperiment explorer},
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author={Rue-Albrecht, Kevin and Marini, Federico and Soneson,
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Charlotte and Lun, Aaron TL},
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journal={F1000Research},
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volume={7},
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year={2018},
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publisher={Faculty of 1000 Ltd}
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}
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</citation>
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</citations>
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</tool>
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