# HG changeset patch
# User bgruening
# Date 1587829441 0
# Node ID 818b16dd05a1a644c74c50afedb72bca13e827f5
# Parent  dc35ae3a672ecba58b56c452205d334147146499
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664"

diff -r dc35ae3a672e -r 818b16dd05a1 macros.xml
--- a/macros.xml	Tue Oct 15 11:58:54 2019 -0400
+++ b/macros.xml	Sat Apr 25 15:44:01 2020 +0000
@@ -4,12 +4,10 @@
     <token name="@IDX_VERSION@">q6</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.0.6">bzip2</requirement>
-            <requirement type="package" version="1.2">seqtk</requirement>
+            <requirement type="package" version="1.3">seqtk</requirement>
             <requirement type="package" version="0.14.1">salmon</requirement>
-            <requirement type="package" version="1.9">samtools</requirement>
+            <requirement type="package" version="1.10">samtools</requirement>
             <requirement type="package" version="0.2.0">vpolo</requirement>
-            <requirement type="package" version="1.17.2">numpy</requirement>
             <requirement type="package" version="0.25.1">pandas</requirement>
             <requirement type="package" version="1.3.1">scipy</requirement>
         </requirements>
@@ -286,6 +284,7 @@
             <citation type="doi">10.1038/nmeth.4197</citation>
         </citations>
     </xml>
+    <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token>
     <token name="@indexing@"><![CDATA[
         mkdir ./index &&
         mkdir ./output &&
diff -r dc35ae3a672e -r 818b16dd05a1 salmonquant.xml
--- a/salmonquant.xml	Tue Oct 15 11:58:54 2019 -0400
+++ b/salmonquant.xml	Sat Apr 25 15:44:01 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="salmon" name="Salmon quant" version="@VERSION@">
+<tool id="salmon" name="Salmon quant" version="@VERSION@+galaxy1">
     <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description>
     <macros>
         <import>macros.xml</import>
@@ -12,15 +12,11 @@
             @salalign@
         #end if
         @salquant@
-        #if $quant_type.qtype == "reads":
-            #if $quant_type.writeMappings:
-                && samtools view -S -b ./output/samout.sam > ./output/bamout.bam
-            #end if
+        #if $quant_type.qtype == "reads" and $quant_type.writeMappings:
+            && @bam_sort@ ./output/samout.sam
         #end if
-        #if $quant_type.qtype == "alignment":
-            #if $quant_type.sampleOut:
-                && samtools sort -@ 4 -o ./output/postSample_sorted.bam ./output/postSample.bam
-            #end if
+        #if $quant_type.qtype == "alignment" and $quant_type.sampleOut:
+            && @bam_sort@ ./output/postSample.bam
         #end if
         ]]>
     </command>
@@ -48,7 +44,7 @@
         <data name="output_bam" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string} (BAM format)">
             <filter>quant_type['qtype'] == "reads" and quant_type['writeMappings']</filter>
         </data>
-        <data name="postSample" format="bam" from_work_dir="./output/postSample_sorted.bam" label="Sampled input alignments on ${on_string}(BAM format)">
+        <data name="postSample" format="bam" from_work_dir="output/bamout.bam" label="Sampled input alignments on ${on_string}(BAM format)">
             <filter>quant_type['qtype'] == "alignment" and quant_type['sampleOut']</filter>
         </data>
     </outputs>