# HG changeset patch
# User iuc
# Date 1566899894 14400
# Node ID 3a1253ee137b829117dc4935d09c85c4b3c5877a
# Parent  e613048778d95769d0e45d07229bdb53c4d181a3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"

diff -r e613048778d9 -r 3a1253ee137b macros.xml
--- a/macros.xml	Sat Aug 17 09:37:54 2019 -0400
+++ b/macros.xml	Tue Aug 27 05:58:14 2019 -0400
@@ -88,7 +88,7 @@
         &&
     #end if
     ]]></token>
-    <token name="@REFGENOMEHANDLING" ><![CDATA[
+    <token name="@REFGENOMEHANDLING@" ><![CDATA[
     --runThreadN \${GALAXY_SLOTS:-4}
     --genomeLoad NoSharedMemory
     --genomeDir
@@ -97,7 +97,7 @@
     #else:
         '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
         ## Handle difference between indices with/without annotations
-        #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
+        #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
             #if $refGenomeSource.GTFconditional.sjdbGTFfile:
                 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
                 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
@@ -114,6 +114,7 @@
             <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
             <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
             <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
+            <yield />
         </stdio>
     </xml>
     <xml name="refgenomehandling" >
@@ -132,10 +133,10 @@
                     </param>
                     <when value="with-gtf">
                         <expand macro="index_selection" with_gene_model="1" />
-                        <expand macro="@SJDBOPTIONS@" />
                     </when>
                     <when value="without-gtf">
                         <expand macro="index_selection" with_gene_model="0" />
+                        <expand macro="@SJDBOPTIONS@" />
                     </when>
                 </conditional>
             </when>
diff -r e613048778d9 -r 3a1253ee137b rg_rnaStarSolo.xml
--- a/rg_rnaStarSolo.xml	Sat Aug 17 09:37:54 2019 -0400
+++ b/rg_rnaStarSolo.xml	Tue Aug 27 05:58:14 2019 -0400
@@ -2,10 +2,12 @@
     <description>mapping, demultiplexing and gene quantification for single cell RNA-seq</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@WRAPPER@"></token>
+        <token name="@WRAPPER@">1</token>
     </macros>
     <expand macro="requirements"/>
-    <expand macro="stdio" />
+    <expand macro="stdio" >
+        <regex match="Segmentation fault" source="both" level="fatal" />
+    </expand>
 
     <command><![CDATA[
     @TEMPINDEX@
@@ -14,8 +16,11 @@
 
     ## cDNA sequence always goes first, then barcode
     --readFilesIn
-    '$input2' '$input1'
-    #if $input1.is_of_type('fastq.gz', 'fastqsanger.gz'):
+    #set $reads2 = ','.join([ '%s' % $x.input2 for $i,$x in enumerate($input_repeats)])
+    #set $reads1 = ','.join([ '%s' % $x.input1 for $i,$x in enumerate($input_repeats)])
+    $reads2 $reads1
+
+    #if $input_repeats[0].input1.is_of_type('fastq.gz', 'fastqsanger.gz'):
         @FASTQ_GZ_OPTION@
     #end if
 
@@ -49,10 +54,11 @@
     --soloUMIdedup '$solo.soloUMIdedup'
     ]]></command>
     <inputs>
-        <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
-        <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, Barcode reads"/>
+        <repeat name="input_repeats" title="Input Pairs" min="1" >
+            <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, Barcode reads"/>
+            <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
+        </repeat>
         <param format="txt,tsv" argument="--soloCBwhitelist" type="data" label="RNA-Seq Cell Barcode Whitelist" />
-
         <expand macro="refgenomehandling" />
         <section name="solo" title="Advanced Settings" expanded="true">
             <conditional name="params">
@@ -106,13 +112,15 @@
     </outputs>
     <tests>
         <test expect_num_outputs="5">
-            <param name="input1" value="41737_R1.fastq.sub240k.gz" ftype="fastqsanger.gz" />
-            <param name="input2" value="41737_R2.fastq.sub240k.gz" ftype="fastqsanger.gz" />
+            <repeat name="input_repeats" >
+                <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" />
+                <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" />
+            </repeat>
             <param name="soloCBwhitelist" value="737K-august-2016.small.txt.gz" />
             <conditional name="refGenomeSource">
                 <param name="geneSource" value="history" />
                 <param name="genomeFastaFiles" value="SNORD83B.22.fa" />
-                <param name="genomeSAindexNbases" value="5" />
+                <param name="genomeSAindexNbases" value="4" />
                 <conditional name="GTFconditional">
                     <param name="GTFselect" value="with-gtf" />
                     <param name="sjdbOverhang" value="75"/>
@@ -145,13 +153,58 @@
             </output>
         </test>
         <test expect_num_outputs="5">
-            <param name="input1" value="41737_R1.fastq.sub240k.gz" ftype="fastqsanger.gz" />
-            <param name="input2" value="41737_R2.fastq.sub240k.gz" ftype="fastqsanger.gz" />
+            <repeat name="input_repeats" >
+                <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" />
+                <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" />
+            </repeat>
             <param name="soloCBwhitelist" value="737K-august-2016.small.txt.gz" />
             <conditional name="refGenomeSource">
                 <param name="geneSource" value="history" />
                 <param name="genomeFastaFiles" value="SNORD83B.22.fa" />
-                <param name="genomeSAindexNbases" value="5" />
+                <param name="genomeSAindexNbases" value="4" />
+                <conditional name="GTFconditional">
+                    <param name="GTFselect" value="with-gtf" />
+                    <param name="sjdbOverhang" value="75" />
+                    <param name="sjdbGTFfile" value="SNORD83B.22.gtf" ftype="gtf"/>
+                </conditional>
+            </conditional>
+            <section name="solo" >
+                <conditional name="params">
+                    <param name="chemistry" value="custom" />
+                    <param name="soloCBstart" value="1" />
+                    <param name="soloCBlen" value="16" />
+                    <param name="soloUMIstart" value="17" />
+                    <param name="soloUMIlen" value="10" />
+                </conditional>
+                <param name="soloStrand" value="Forward" />
+                <param name="soloFeatures" value="GeneFull" />
+                <param name="soloUMIdedup" value="1MM_Directional" />
+            </section>
+            <output name="output_barcodes" >
+                <assert_contents>
+                    <has_line line="TTTGTCATCTTAGAGC" />
+                    <has_line line="TTTGTCATCTTTCCTC" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="5">
+            <repeat name="input_repeats" >
+                <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" />
+                <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" />
+            </repeat>
+            <repeat name="input_repeats" >
+                <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" />
+                <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" />
+            </repeat>
+            <repeat name="input_repeats" >
+                <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" />
+                <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" />
+            </repeat>
+            <param name="soloCBwhitelist" value="737K-august-2016.small.txt.gz" />
+            <conditional name="refGenomeSource">
+                <param name="geneSource" value="history" />
+                <param name="genomeFastaFiles" value="SNORD83B.22.fa" />
+                <param name="genomeSAindexNbases" value="4" />
                 <conditional name="GTFconditional">
                     <param name="GTFselect" value="with-gtf" />
                     <param name="sjdbOverhang" value="75" />
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