| Next changeset 1:2062be7efc84 (2023-12-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ commit e83761e8057df5ce516fc6681636435078c81534 |
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added:
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 |
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| diff -r 000000000000 -r d70139524747 sceasy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sceasy.xml Fri Nov 10 20:24:21 2023 +0000 |
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| b'@@ -0,0 +1,224 @@\n+<tool id="sceasy_convert" name="SCEasy Converter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">\n+ <description>\n+ Convert between common single cell formats\n+ </description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">0.0.7</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n+ <macro name="mac_input_form" token_format="@FORMAT@" >\n+ <param name="input_object_file" type="data" format="@FORMAT@" label="Input object in @FORMAT@ format"/>\n+ </macro>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="0.0.7">r-sceasy</requirement>\n+ <requirement type="package" version="3.0.6" >loompy</requirement>\n+ <requirement type="package" version="0.10.0" >anndata</requirement>\n+ <requirement type="package" version="3.10" >python</requirement>\n+ <requirement type="package" version="0.7.5.4" >r-anndata</requirement>\n+ <requirement type="package" version="1.32.0" >r-reticulate</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code">\n+ Rscript \'$script_file\'\n+ </command>\n+ <configfiles>\n+ <configfile name="script_file"><![CDATA[\n+direction=\'$conversion.direction\'\n+tokens = unlist(strsplit(direction, split="2"))\n+format.from = tokens[1]\n+format.to = tokens[2]\n+\n+library(sceasy)\n+library(reticulate)\n+\n+## HACK: CI biocontainers do not contain a useable conda binary, just the env.\n+## see: https://github.com/galaxyproject/tools-iuc/issues/5585#issuecomment-1803773923\n+is_biocontainer = grepl("^# cmd: /opt/conda/bin/",\n+ paste0(reticulate:::python_info_condaenv_find("/usr/local/"),\n+ "-none"))\n+if (is_biocontainer) {\n+ ## conda detection false positive\n+ assignInNamespace("is_conda_python", function(x) FALSE, ns="reticulate")\n+ use_python("/usr/local/bin/python")\n+} else {\n+ conda_path = Sys.getenv("CONDA_PREFIX")\n+ if (conda_path != "") {\n+ ## Active conda env found\n+ use_python(file.path(conda_path, "bin", "python3"))\n+ } else {\n+ ## Not biocontainer or conda, assume system python\n+ use_python("/usr/bin/python3")\n+ }\n+}\n+loompy = reticulate::import(\'loompy\')\n+infile = \'$input_object_file\'\n+\n+outfile_ext_map=list(\n+ "anndata" = "h5ad",\n+ "seurat" = "rds",\n+ "sce" = "rds",\n+ "cds" = "rds",\n+ "loom" = "loom") ## this has to be a .loom ending for the export to work.\n+\n+outfile = paste0("outfile.", outfile_ext_map[format.to])\n+\n+\n+## IDIOSYNCRACIES:\n+## Some input formats need be loaded first and then converted,\n+## and other formats need to be specified as filenames only,\n+## and even then as formats with specific extensions,\n+## and some formats need to be objects, or stripped down objects,\n+## and probably more issues will be discovered in time.\n+\n+do_infile_as_first_arg = as.logical(direction == "loom2sce")\n+do_filename_as_first_arg = as.logical(direction %in% c("anndata2cds", "anndata2seurat", "loom2anndata"))\n+do_dietseurat_in_first_arg = as.logical(direction == "seurat2sce")\n+\n+if (do_infile_as_first_arg) {\n+ if (format.from == "loom") {\n+ ## LoomExperiment::import only correctly imports when ext is set\n+ loom_file = tempfile(tmpdir="/tmp", fileext=".loom")\n+ file.copy(from=infile, to=loom_file) ## rename doesn\'t work in containers\n+ infile = loom_file\n+ }\n+ convertFormat(inFile = infile, from = format.from, to = format.to, outFile = outfile)\n+} else if (do_filename_as_first_arg) {\n+ convertFormat(infile, from = format.from, to = format.to, outFile = outfile)\n+} else {\n+ ## We need to physically load the object (either Seurat or SCE, both which should be\n+ ## of RDS input type)\n+ rds = readRDS(infile)\n+\n+ if (do_dietseurat_in_first_arg){\n+ library(Seurat)\n+ rds = DietSeurat(rds)\n+ }\n+ convertFormat(rds, from = format.from, to = format.to, outFile = outfile)\n+}\n+\n+ ]]></configfile>\n+ </config'..b'" token_format="rds" />\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data name="output_sce" format="rdata" from_work_dir="outfile.rds" label="${tool.name} on ${on_string}: SingleCellExperiment">\n+ <filter>\n+ conversion[\'direction\'].endswith(\'sce\')\n+ </filter>\n+ </data>\n+ <data name="output_cds" format="rdata" from_work_dir="outfile.rds" label="${tool.name} on ${on_string}: CellDataSet">\n+ <filter>\n+ conversion[\'direction\'].endswith(\'cds\')\n+ </filter>\n+ </data>\n+ <data name="output_loom" format="h5" from_work_dir="outfile.loom" label="${tool.name} on ${on_string}: Loom">\n+ <filter>\n+ conversion[\'direction\'].endswith(\'loom\')\n+ </filter>\n+ </data>\n+ <data name="output_anndata" format="h5" from_work_dir="outfile.h5ad" label="${tool.name} on ${on_string}: AnnData">\n+ <filter>\n+ conversion[\'direction\'].endswith(\'anndata\')\n+ </filter>\n+ </data>\n+ <data name="output_seurat" format="rdata" from_work_dir="outfile.rds" label="${tool.name} on ${on_string}: Seurat">\n+ <filter>\n+ conversion[\'direction\'].endswith(\'seurat\')\n+ </filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="1">\n+ <param name="direction" value="anndata2cds"/>\n+ <param name="input_object_file" value="test_anndata.h5ad"/>\n+ <output name="output_cds" file="ad2cds.rds" ftype="rdata" compare="sim_size"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="direction" value="anndata2seurat"/>\n+ <param name="input_object_file" value="test_anndata.h5ad"/>\n+ <output name="output_seurat" file="ad2seurat.rds" ftype="rdata" compare="sim_size"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="direction" value="loom2anndata"/>\n+ <param name="input_object_file" value="sce2loom.rds"/>\n+ <output name="output_anndata" file="loom2anndata.h5ad" ftype="h5" compare="sim_size"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="direction" value="loom2sce"/>\n+ <param name="input_object_file" value="sce2loom.rds"/>\n+ <output name="output_sce" file="loom2sce.rds" ftype="rdata" compare="sim_size"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="direction" value="sce2anndata"/>\n+ <param name="input_object_file" value="test_sce.rds"/>\n+ <output name="output_anndata" file="sce2anndata.h5ad" ftype="h5" compare="sim_size"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="direction" value="sce2loom"/>\n+ <param name="input_object_file" value="test_sce.rds"/>\n+ <output name="output_loom" file="sce2loom.rds" ftype="h5" compare="sim_size"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="direction" value="seurat2anndata"/>\n+ <param name="input_object_file" value="test_seurat.rds"/>\n+ <output name="output_seurat" file="test_anndata.h5ad" ftype="h5" compare="sim_size"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="direction" value="seurat2sce"/>\n+ <param name="input_object_file" value="test_seurat.rds"/>\n+ <output name="output_sce" file="test_sce.rds" ftype="rdata" compare="sim_size"/>\n+ </test>\n+ </tests>\n+ <help>\n+SCeasy\n+======\n+\n+ Convert scRNA data object between formats `sceasy::convertFormat()`\n+\n+Supports the following conversion:\n+\n+.. image:: $PATH_TO_IMAGES/conv.png\n+\t:width: 80 %\n+\t:align: center\n+\n+\n+ </help>\n+ <citations>\n+ <citation type="doi"> doi:10.1093/nargab/lqaa052</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
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