# HG changeset patch
# User iuc
# Date 1632216801 0
# Node ID 0a86e1e47784d0ed1b07af536808e1f2fab15d13
# Parent  6fc18540551243549c4ceac278e885837839a887
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit a18f79e7cfe15fd6e1a5f70533616c379e4e7c6a"

diff -r 6fc185405512 -r 0a86e1e47784 macros.xml
--- a/macros.xml	Sun Jul 28 14:49:11 2019 -0400
+++ b/macros.xml	Tue Sep 21 09:33:21 2021 +0000
@@ -77,18 +77,18 @@
        <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> 
     </xml>
     <xml name="flag_options">
-        <option value="1">read is paired</option>
-        <option value="2">read is mapped in a proper pair</option>
-        <option value="4">read is unmapped</option>
-        <option value="8">mate is unmapped</option>
-        <option value="16">read reverse strand</option>
-        <option value="32">mate reverse strand</option>
-        <option value="64">read is the first in a pair</option>
-        <option value="128">read is the second in a pair</option>
-        <option value="256">alignment or read is not primary</option>
-        <option value="512">read fails platform/vendor quality checks</option>
-        <option value="1024">read is a PCR or optical duplicate</option>
-        <option value="2048">supplementary alignment</option>
+        <option value="1">Read is paired</option>
+        <option value="2">Read is mapped in a proper pair</option>
+        <option value="4">Read is unmapped</option>
+        <option value="8">Mate is unmapped</option>
+        <option value="16">Read is mapped to the reverse strand of the reference</option>
+        <option value="32">Mate is mapped to the reverse strand of the reference</option>
+        <option value="64">Read is the first in a pair</option>
+        <option value="128">Read is the second in a pair</option>
+        <option value="256">Alignment of the read is not primary</option>
+        <option value="512">Read fails platform/vendor quality checks</option>
+        <option value="1024">Read is a PCR or optical duplicate</option>
+        <option value="2048">Alignment is supplementary</option>
     </xml>
 
     <!-- region specification macros and tokens for tools that allow the specification 
diff -r 6fc185405512 -r 0a86e1e47784 samtools_mpileup.xml
--- a/samtools_mpileup.xml	Sun Jul 28 14:49:11 2019 -0400
+++ b/samtools_mpileup.xml	Tue Sep 21 09:33:21 2021 +0000
@@ -12,16 +12,15 @@
     @PREPARE_IDX_MULTIPLE@
 
     #if $reference_source.reference_source_selector == "history":
-        ln -s '${reference_source.ref_file}' &&
-        samtools faidx `basename '${reference_source.ref_file}'` &&
+        #set ref_fa = 'ref.fa'
+        ln -s '${reference_source.ref_file}' 'ref.fa' &&
+        samtools faidx ref.fa &&
+    #else:
+        #set ref_fa = str( $reference_source.ref_file.fields.path )
     #end if
 
     samtools mpileup
-    #if $reference_source.reference_source_selector != "history":
-        -f '${reference_source.ref_file.fields.path}'
-    #else:
-        -f '${reference_source.ref_file}'
-    #end if
+        -f '$ref_fa'
     #for $i in range(len( $input_bams )):
         '${i}'
     #end for