Mercurial > repos > iuc > dropletutils
changeset 5:cdf4443d5625 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7"
| author | iuc |
|---|---|
| date | Wed, 29 Jan 2020 15:07:38 -0500 |
| parents | 1797cbe967d1 |
| children | 8855361fcfc5 |
| files | dropletutils.xml scripts/dropletutils.Rscript test-data/defs_defaultdrops.h5 test-data/defs_defaultdrops.h5ad test-data/defs_emptydrops_150_0002.h5 test-data/defs_emptydrops_150_0002.h5ad test-data/defs_emptydrops_150_0002a.h5 test-data/defs_emptydrops_150_0002a.h5ad test-data/in_matrix.h5 test-data/in_matrix.h5ad |
| diffstat | 10 files changed, 22 insertions(+), 22 deletions(-) [+] |
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--- a/dropletutils.xml Thu Dec 05 01:32:29 2019 -0500 +++ b/dropletutils.xml Wed Jan 29 15:07:38 2020 -0500 @@ -3,7 +3,7 @@ <description>Utilities for handling droplet-based single-cell RNA-seq data</description> <macros> <token name="@PACKAGE_VERSION@" >1.2.1</token> - <token name="@GALAXY_VERSION@" >5</token> + <token name="@GALAXY_VERSION@" >galaxy6</token> <token name="@TXIN@">tenx.input</token> <token name="@TXOUT@">tenx.output</token> <xml name="test_dirin" > @@ -80,8 +80,8 @@ out.type='$operation.outformat' #if str($operation.outformat) == 'directory': files\$out='@TXOUT@' - #else if str($operation.outformat) == 'h5ad': -files\$out='$fileout_h5ad' + #else if str($operation.outformat) == 'h5': +files\$out='$fileout_h5' #else if str($operation.outformat) == 'tsv': files\$out='$fileout_tsv' #end if @@ -99,7 +99,7 @@ <conditional name="tenx_format"> <param name="use" type="select" label="Format for the input matrix"> <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option> - <option value="h5ad" selected="true" >AnnData/H5</option> + <option value="h5" selected="true" >H5</option> <option value="tsv">Tabular</option> </param> <when value="directory"> @@ -107,8 +107,8 @@ <param name="input_genes" type="data" format="tabular,tsv,txt" label="Genes List"/> <param name="input_barcodes" type="data" format="tabular,tsv,txt" label="Barcodes List"/> </when> - <when value="h5ad"> - <param name="input" type="data" format="h5ad" label="Count Data"/> + <when value="h5"> + <param name="input" type="data" format="h5" label="Count Data"/> </when> <when value="tsv"> <param name="input" type="data" format="tabular,tsv" label="Count Data" help="The first column must contain gene names, and the first row must contain barcode identifiers." /> @@ -137,7 +137,7 @@ </conditional> <param name="outformat" type="select" label="Format for output matrices"> <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option> - <option value="h5ad" selected="true" >AnnData/H5</option> + <option value="h5" selected="true" >H5</option> <option value="tsv">Tabular</option> </param> </when> @@ -151,8 +151,8 @@ <data name="fileout_tsv" format="tsv" label="${tool.name} Count Matrix on ${on_string}"> <filter>operation['use']=='filter' and operation['outformat'] == 'tsv' </filter> </data> - <data name="fileout_h5ad" format="h5ad" label="${tool.name} AnnData on ${on_string}"> - <filter>operation['use']=='filter' and operation['outformat'] == 'h5ad'</filter> + <data name="fileout_h5" format="h5" label="${tool.name} H5 Matrix on ${on_string}"> + <filter>operation['use']=='filter' and operation['outformat'] == 'h5'</filter> </data> <data name="barcodes_out" format="tsv" from_work_dir="@TXOUT@/barcodes.tsv" label="${tool.name} 10X Barcodes on ${on_string}" > <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter> @@ -177,9 +177,9 @@ <expand macro="test_dirin" /> <conditional name="operation"> <param name="use" value="filter" /> - <param name="outformat" value="h5ad" /><!-- H5AD --> + <param name="outformat" value="h5" /><!-- H5 --> </conditional> - <output name="fileout_h5ad" value="defs_defaultdrops.h5ad" compare="sim_size" delta="10" /> + <output name="fileout_h5" value="defs_defaultdrops.h5" compare="sim_size" delta="10" /> </test> <test expect_num_outputs="1"> <expand macro="test_dirin" /> @@ -210,14 +210,14 @@ <expand macro="test_dirin" /> <conditional name="operation"> <param name="use" value="filter" /> - <param name="outformat" value="h5ad" /> + <param name="outformat" value="h5" /> <conditional name="method"> <param name="use" value="emptydrops" /> <param name="lower" value="150" /> <param name="fdr_thresh" value="0.02" /> </conditional> </conditional> - <output name="fileout_h5ad" value="defs_emptydrops_150_0002.h5ad" compare="sim_size" delta="10" /> + <output name="fileout_h5" value="defs_emptydrops_150_0002.h5" compare="sim_size" delta="10" /> <output name="table" > <assert_contents> <has_n_columns n="9" /> @@ -229,22 +229,22 @@ <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" /> </test> <!-- Other format input tests --> - <!-- ::: Empty Drops, same as above but input is h5ad --> + <!-- ::: Empty Drops, same as above but input is h5 --> <test expect_num_outputs="3"> <conditional name="tenx_format" > - <param name="use" value="h5ad" /> - <param name="input" value="in_matrix.h5ad" /> + <param name="use" value="h5" /> + <param name="input" value="in_matrix.h5" /> </conditional> <conditional name="operation"> <param name="use" value="filter" /> - <param name="outformat" value="h5ad" /> + <param name="outformat" value="h5" /> <conditional name="method"> <param name="use" value="emptydrops" /> <param name="lower" value="150" /> <param name="fdr_thresh" value="0.02" /> </conditional> </conditional> - <output name="fileout_h5ad" value="defs_emptydrops_150_0002a.h5ad" compare="sim_size" delta="400" /> + <output name="fileout_h5" value="defs_emptydrops_150_0002a.h5" compare="sim_size" delta="400" /> <output name="table" > <assert_contents> <has_n_columns n="9" />
--- a/scripts/dropletutils.Rscript Thu Dec 05 01:32:29 2019 -0500 +++ b/scripts/dropletutils.Rscript Wed Jan 29 15:07:38 2020 -0500 @@ -34,7 +34,7 @@ if (typeout == "tsv"){ writeTSV(fileout, getCounts(object)) } - else if (typeout == "h5ad"){ + else if (typeout == "h5"){ write10xCounts(fileout, getCounts(object), type="HDF5", gene.symbol=determineGeneIDs(object), @@ -55,7 +55,7 @@ ## - solution is to use the readSparseCounts function from scater sce <- SingleCellExperiment(assays = list(counts = readSparseCounts(filein))) } - else if (typein == "h5ad"){ + else if (typein == "h5"){ sce <- read10xCounts(filein, col.names=T, type="HDF5") # use barcodes.tsv as column names } else if (typein == "directory"){ @@ -69,7 +69,7 @@ ## Methods -doEmptyDrops <- function(files, eparams, in.type="directory", out.type="h5ad", fdr_threshold = 0.01){ +doEmptyDrops <- function(files, eparams, in.type="directory", out.type="h5", fdr_threshold = 0.01){ sce <- read10xFiles(files$infile, in.type) eparams$... <- NULL ## hack @@ -115,7 +115,7 @@ } -doDefaultDrops <- function(files, dparams, in.type="directory", out.type="h5ad"){ +doDefaultDrops <- function(files, dparams, in.type="directory", out.type="h5"){ sce <- read10xFiles(files$infile, in.type) dparams$m = counts(sce)