| Previous changeset 0:b4332c428c63 (2019-11-11) Next changeset 2:00b41600e1c1 (2020-03-16) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit fb1feb9e744358eed6c2b5583cea433a00889495 |
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modified:
dropletutils-empty-drops.xml |
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| diff -r b4332c428c63 -r da189ce4016b dropletutils-empty-drops.xml --- a/dropletutils-empty-drops.xml Mon Nov 11 05:52:59 2019 -0500 +++ b/dropletutils-empty-drops.xml Thu Nov 21 09:41:50 2019 -0500 |
| [ |
| @@ -1,12 +1,12 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="dropletutils_empty_drops" name="DropletUtils emptyDrops" version="@TOOL_VERSION@+galaxy0"> +<tool id="dropletutils_empty_drops" name="DropletUtils emptyDrops" version="@TOOL_VERSION@+galaxy1"> <description>Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment.</description> <macros> <import>dropletutils_macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - dropletutils-empty-drops.R --input-object-file "${input}" --output-object-file "${output_rds}" --output-text-file "${output_txt}" --lower "${lower}" --niters "${niters}" --filter-fdr "${filter_fdr}" --test-ambient "${testambient}" --filter-empty "${filter_empty}" + dropletutils-empty-drops.R --input-object-file "${input}" --output-object-file "${output_rdata}" --output-text-file "${output_txt}" --lower "${lower}" --niters "${niters}" --filter-fdr "${filter_fdr}" --test-ambient "${testambient}" --filter-empty "${filter_empty}" #if $ignore != '' --ignore $ignore #end if @@ -16,7 +16,7 @@ ]]></command> <inputs> - <param name="input" argument="--input-object-file" type="data" format="rdata" label="SingleCellExperiment RDS object" help="e.g. Output from DropletUtils Read10x." /> + <param name="input" argument="--input-object-file" type="data" format="rdata" label="SingleCellExperiment rdata object" help="e.g. Output from DropletUtils Read10x." /> <param name="lower" argument="--lower" type="integer" optional="True" label="UMI count lower bound" value='100' help="A numeric scalar specifying the lower bound on the total UMI count, at or below which all barcodes are assumed to correspond to empty droplets." /> <param name="niters" argument="--niters" type="integer" optional="True" value='1000' label="Number of iterations" help="An integer scalar specifying the number of iterations to use for the Monte Carlo p-value calculations." /> <param name="filter_fdr" argument="--filter-fdr" type="float" value='0.01' label="FDR filter for removal of barcodes with no cells" /> @@ -27,7 +27,7 @@ </inputs> <outputs> - <data name="output_rds" format="rdata" label="${tool.name} on ${on_string}: serialized SingleCellExperiment object"/> + <data name="output_rdata" format="rdata" label="${tool.name} on ${on_string}: serialized SingleCellExperiment object"/> <data name="output_txt" format="txt" label="${tool.name} on ${on_string}: tabular output"/> </outputs> |