# HG changeset patch
# User iuc
# Date 1602859113 0
# Node ID 3ffca09599cae31797d454ee3a0625ccc02775f1
# Parent  7397e6badc113b6d7f4ae860ff60d200bf2a905f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7"

diff -r 7397e6badc11 -r 3ffca09599ca scpipe.xml
--- a/scpipe.xml	Thu Jun 11 07:18:37 2020 -0400
+++ b/scpipe.xml	Fri Oct 16 14:38:33 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="scpipe" name="scPipe" version="1.0.0+galaxy1">
+<tool id="scpipe" name="scPipe" version="1.0.0+galaxy2" profile="19.01">
     <description>- preprocessing pipeline for single cell RNA-seq</description>
     <requirements>
         <requirement type="package" version="1.0.0">bioconductor-scpipe</requirement>
@@ -74,7 +74,7 @@
 TAB=\$(printf '\t') &&
 
 #if $samples.barcodes:
-    sed -i.bak -e "s/\${TAB}/,/g" '$samples.barcodes' &&
+    sed -e "s/\${TAB}/,/g" '$samples.barcodes' > samples.barcodes &&
 #end if
 
 ## Run scPipe
@@ -84,14 +84,14 @@
 #if $samples.format_select == "bam":
     --bam '$bam_name'
     --samplename '$bam_name'
-    --barcodes '$samples.barcodes'
+    --barcodes 'samples.barcodes'
 #else:
     --fasta '$fasta_name'
     --read1 '$in1_name'
     --read2 '$in2_name'
     --samplename '$in1_name'
-    #if $barcodes:
-        --barcodes '$samples.barcodes'
+    #if $samples.barcodes:
+        --barcodes 'samples.barcodes'
     #end if
 #end if
 
@@ -244,8 +244,8 @@
         <test>
             <param name="format_select" value="fastq" />
             <param name="fasta_source" value="history"/>
-            <param name="ref_fa_hist" ftype="fasta" value="mm10_MT19.fa.gz"/>
-            <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/>
+            <param name="ref_fa_hist" ftype="fasta.gz" value="mm10_MT19.fa.gz"/>
+            <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/>
             <param name="organism" value="mmusculus_gene_ensembl"/>
             <param name="paired_format_selector" value="paired" />
             <param name="in1" ftype="fastqsanger.gz" value="CB51_MT19_R1.gz"/>
@@ -269,7 +269,7 @@
         <test>
             <param name="format_select" value="fastq" />
             <param name="fasta_source" value="cached"/>
-            <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/>
+            <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/>
             <param name="organism" value="mmusculus_gene_ensembl"/>
             <param name="paired_format_selector" value="paired" />
             <param name="in1" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R1.gz"/>
@@ -288,7 +288,7 @@
             <param name="format_select" value="bam" />
             <param name="bam" ftype="bam" value="aligned.mapped.bam"/>
             <param name="barcodes" ftype="tabular" value="barcode_anno.tsv"/>
-            <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/>
+            <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/>
             <param name="organism" value="mmusculus_gene_ensembl"/>
             <param name="us" value="-1"/>
             <output name="out_matrix" >
@@ -302,7 +302,7 @@
             <param name="format_select" value="bam" />
             <param name="bam" ftype="bam" value="aligned.mapped.bam"/>
             <param name="barcodes" ftype="tabular" value="barcode_anno.tsv"/>
-            <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/>
+            <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/>
             <param name="organism" value="mmusculus_gene_ensembl"/>
             <param name="us" value="-1"/>
             <param name="plots" value="True"/>