# HG changeset patch
# User iuc
# Date 1626630859 0
# Node ID c971db6f0fe5c5572115bf1bd620122c047af284
# Parent  40985510cd98f2dbfd061886b5d808d62a1c4752
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c657f8cc0308cd70b26e3b111e5d8008901cda24"

diff -r 40985510cd98 -r c971db6f0fe5 kallisto_quant.xml
--- a/kallisto_quant.xml	Tue Apr 06 21:07:57 2021 +0000
+++ b/kallisto_quant.xml	Sun Jul 18 17:54:19 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.4">
+<tool id="kallisto_quant" name="Kallisto quant" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>- quantify abundances of RNA-Seq transcripts</description>
     <macros>
         <import>macros.xml</import>
@@ -40,7 +40,7 @@
                 $reads
             #end if
             #if $pseudobam:
-                | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$pseudobam_output' -
+                && samtools sort --no-PG -O bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$pseudobam_output' pseudoalignments.bam
             #end if
             && cat run_info.json
         ]]>
@@ -148,7 +148,7 @@
             <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />
             <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />
             <output name="abundance_tab" file="kallisto_quant_out4.tab" ftype="tabular" />
-            <output name="pseudobam_output" file="kallisto_quant_out4.bam" ftype="bam" />
+            <output name="pseudobam_output" file="kallisto_quant_out4.bam" ftype="bam" lines_diff="2"/>
         </test>
         <test>
             <param name="reference_transcriptome_source" value="cached" />
@@ -158,7 +158,7 @@
             <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
             <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />
             <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" />
-            <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" />
+            <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" lines_diff="2"/>
         </test>
         <test>
             <param name="reference_transcriptome_source" value="history" />
diff -r 40985510cd98 -r c971db6f0fe5 macros.xml
--- a/macros.xml	Tue Apr 06 21:07:57 2021 +0000
+++ b/macros.xml	Sun Jul 18 17:54:19 2021 +0000
@@ -1,10 +1,11 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">0.46.0</token>
+    <token name="@TOOL_VERSION@">0.46.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">kallisto</requirement>
-            <requirement type="package" version="1.9">samtools</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">kallisto</requirement>
+            <requirement type="package" version="1.12">samtools</requirement>
         </requirements>
     </xml>
     <xml name="citations">
diff -r 40985510cd98 -r c971db6f0fe5 test-data/kallisto_quant_out4.bam
Binary file test-data/kallisto_quant_out4.bam has changed
diff -r 40985510cd98 -r c971db6f0fe5 test-data/kallisto_quant_out5.bam
Binary file test-data/kallisto_quant_out5.bam has changed