changeset 1:da189ce4016b draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit fb1feb9e744358eed6c2b5583cea433a00889495

--- 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>