Mercurial > repos > iuc > sceasy_convert
changeset 0:d70139524747 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ commit e83761e8057df5ce516fc6681636435078c81534
| author | iuc |
|---|---|
| date | Fri, 10 Nov 2023 20:24:21 +0000 |
| parents | |
| children | 2062be7efc84 |
| files | sceasy.xml static/images/conv.png test-data/ad2cds.rds test-data/ad2seurat.rds test-data/loom2anndata.h5ad test-data/loom2sce.rds test-data/sce2anndata.h5ad test-data/sce2loom.rds test-data/test_anndata.h5ad test-data/test_sce.rds test-data/test_seurat.rds |
| diffstat | 11 files changed, 224 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sceasy.xml Fri Nov 10 20:24:21 2023 +0000 @@ -0,0 +1,224 @@ +<tool id="sceasy_convert" name="SCEasy Converter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> + <description> + Convert between common single cell formats + </description> + <macros> + <token name="@TOOL_VERSION@">0.0.7</token> + <token name="@VERSION_SUFFIX@">1</token> + <macro name="mac_input_form" token_format="@FORMAT@" > + <param name="input_object_file" type="data" format="@FORMAT@" label="Input object in @FORMAT@ format"/> + </macro> + </macros> + <requirements> + <requirement type="package" version="0.0.7">r-sceasy</requirement> + <requirement type="package" version="3.0.6" >loompy</requirement> + <requirement type="package" version="0.10.0" >anndata</requirement> + <requirement type="package" version="3.10" >python</requirement> + <requirement type="package" version="0.7.5.4" >r-anndata</requirement> + <requirement type="package" version="1.32.0" >r-reticulate</requirement> + </requirements> + <command detect_errors="exit_code"> + Rscript '$script_file' + </command> + <configfiles> + <configfile name="script_file"><![CDATA[ +direction='$conversion.direction' +tokens = unlist(strsplit(direction, split="2")) +format.from = tokens[1] +format.to = tokens[2] + +library(sceasy) +library(reticulate) + +## HACK: CI biocontainers do not contain a useable conda binary, just the env. +## see: https://github.com/galaxyproject/tools-iuc/issues/5585#issuecomment-1803773923 +is_biocontainer = grepl("^# cmd: /opt/conda/bin/", + paste0(reticulate:::python_info_condaenv_find("/usr/local/"), + "-none")) +if (is_biocontainer) { + ## conda detection false positive + assignInNamespace("is_conda_python", function(x) FALSE, ns="reticulate") + use_python("/usr/local/bin/python") +} else { + conda_path = Sys.getenv("CONDA_PREFIX") + if (conda_path != "") { + ## Active conda env found + use_python(file.path(conda_path, "bin", "python3")) + } else { + ## Not biocontainer or conda, assume system python + use_python("/usr/bin/python3") + } +} +loompy = reticulate::import('loompy') +infile = '$input_object_file' + +outfile_ext_map=list( + "anndata" = "h5ad", + "seurat" = "rds", + "sce" = "rds", + "cds" = "rds", + "loom" = "loom") ## this has to be a .loom ending for the export to work. + +outfile = paste0("outfile.", outfile_ext_map[format.to]) + + +## IDIOSYNCRACIES: +## Some input formats need be loaded first and then converted, +## and other formats need to be specified as filenames only, +## and even then as formats with specific extensions, +## and some formats need to be objects, or stripped down objects, +## and probably more issues will be discovered in time. + +do_infile_as_first_arg = as.logical(direction == "loom2sce") +do_filename_as_first_arg = as.logical(direction %in% c("anndata2cds", "anndata2seurat", "loom2anndata")) +do_dietseurat_in_first_arg = as.logical(direction == "seurat2sce") + +if (do_infile_as_first_arg) { + if (format.from == "loom") { + ## LoomExperiment::import only correctly imports when ext is set + loom_file = tempfile(tmpdir="/tmp", fileext=".loom") + file.copy(from=infile, to=loom_file) ## rename doesn't work in containers + infile = loom_file + } + convertFormat(inFile = infile, from = format.from, to = format.to, outFile = outfile) +} else if (do_filename_as_first_arg) { + convertFormat(infile, from = format.from, to = format.to, outFile = outfile) +} else { + ## We need to physically load the object (either Seurat or SCE, both which should be + ## of RDS input type) + rds = readRDS(infile) + + if (do_dietseurat_in_first_arg){ + library(Seurat) + rds = DietSeurat(rds) + } + convertFormat(rds, from = format.from, to = format.to, outFile = outfile) +} + + ]]></configfile> + </configfiles> + <inputs> + <conditional name="conversion" > + <param name="direction" type="select" label="Convert From / To" > + <option value="anndata2cds" >AnnData to CellDataSet</option> + <option value="anndata2seurat" >AnnData to Seurat</option> + <option value="loom2anndata" >Loom to AnnData</option> + <option value="loom2sce">Loom to SingleCellexperiment</option> + <option value="sce2anndata" >SingleCellexperiment to AnnData</option> + <option value="sce2loom" >SingleCellexperiment to Loom</option> + <option value="seurat2anndata">Seurat to AnnData</option> + <option value="seurat2sce" >Seurat to SingleCellexperiment</option> + </param> + <when value="anndata2cds" > + <expand macro="mac_input_form" token_format="h5ad" /> + </when> + <when value="anndata2seurat" > + <expand macro="mac_input_form" token_format="h5ad" /> + </when> + <when value="loom2anndata"> + <expand macro="mac_input_form" token_format="h5" /> + </when> + <when value="loom2sce"> + <expand macro="mac_input_form" token_format="h5" /> + </when> + <when value="sce2anndata"> + <expand macro="mac_input_form" token_format="sce" /> + </when> + <when value="sce2loom"> + <expand macro="mac_input_form" token_format="sce" /> + </when> + <when value="seurat2anndata"> + <expand macro="mac_input_form" token_format="rds" /> + </when> + <when value="seurat2sce"> + <expand macro="mac_input_form" token_format="rds" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="output_sce" format="rdata" from_work_dir="outfile.rds" label="${tool.name} on ${on_string}: SingleCellExperiment"> + <filter> + conversion['direction'].endswith('sce') + </filter> + </data> + <data name="output_cds" format="rdata" from_work_dir="outfile.rds" label="${tool.name} on ${on_string}: CellDataSet"> + <filter> + conversion['direction'].endswith('cds') + </filter> + </data> + <data name="output_loom" format="h5" from_work_dir="outfile.loom" label="${tool.name} on ${on_string}: Loom"> + <filter> + conversion['direction'].endswith('loom') + </filter> + </data> + <data name="output_anndata" format="h5" from_work_dir="outfile.h5ad" label="${tool.name} on ${on_string}: AnnData"> + <filter> + conversion['direction'].endswith('anndata') + </filter> + </data> + <data name="output_seurat" format="rdata" from_work_dir="outfile.rds" label="${tool.name} on ${on_string}: Seurat"> + <filter> + conversion['direction'].endswith('seurat') + </filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="direction" value="anndata2cds"/> + <param name="input_object_file" value="test_anndata.h5ad"/> + <output name="output_cds" file="ad2cds.rds" ftype="rdata" compare="sim_size"/> + </test> + <test expect_num_outputs="1"> + <param name="direction" value="anndata2seurat"/> + <param name="input_object_file" value="test_anndata.h5ad"/> + <output name="output_seurat" file="ad2seurat.rds" ftype="rdata" compare="sim_size"/> + </test> + <test expect_num_outputs="1"> + <param name="direction" value="loom2anndata"/> + <param name="input_object_file" value="sce2loom.rds"/> + <output name="output_anndata" file="loom2anndata.h5ad" ftype="h5" compare="sim_size"/> + </test> + <test expect_num_outputs="1"> + <param name="direction" value="loom2sce"/> + <param name="input_object_file" value="sce2loom.rds"/> + <output name="output_sce" file="loom2sce.rds" ftype="rdata" compare="sim_size"/> + </test> + <test expect_num_outputs="1"> + <param name="direction" value="sce2anndata"/> + <param name="input_object_file" value="test_sce.rds"/> + <output name="output_anndata" file="sce2anndata.h5ad" ftype="h5" compare="sim_size"/> + </test> + <test expect_num_outputs="1"> + <param name="direction" value="sce2loom"/> + <param name="input_object_file" value="test_sce.rds"/> + <output name="output_loom" file="sce2loom.rds" ftype="h5" compare="sim_size"/> + </test> + <test expect_num_outputs="1"> + <param name="direction" value="seurat2anndata"/> + <param name="input_object_file" value="test_seurat.rds"/> + <output name="output_seurat" file="test_anndata.h5ad" ftype="h5" compare="sim_size"/> + </test> + <test expect_num_outputs="1"> + <param name="direction" value="seurat2sce"/> + <param name="input_object_file" value="test_seurat.rds"/> + <output name="output_sce" file="test_sce.rds" ftype="rdata" compare="sim_size"/> + </test> + </tests> + <help> +SCeasy +====== + + Convert scRNA data object between formats `sceasy::convertFormat()` + +Supports the following conversion: + +.. image:: $PATH_TO_IMAGES/conv.png + :width: 80 % + :align: center + + + </help> + <citations> + <citation type="doi"> doi:10.1093/nargab/lqaa052</citation> + </citations> +</tool> \ No newline at end of file