# HG changeset patch
# User iuc
# Date 1708889419 0
# Node ID 27673f5b534369574273808f03c782ab2d7757d0
# Parent  359e043a285c12fd91593ec8569586ef84ca8f35
planemo upload for repository https://github.com/davebx/bioext-gx/ commit 473fd4bfc9bc6dc149978013545525529978b988

diff -r 359e043a285c -r 27673f5b5343 bam2msa.xml
--- a/bam2msa.xml	Mon Nov 08 11:40:50 2021 +0000
+++ b/bam2msa.xml	Sun Feb 25 19:30:19 2024 +0000
@@ -3,18 +3,18 @@
     <description>to FASTA multiple sequence alignment</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         ## avoid bam2msa to create .bai in inputdir
-        ln -s '$input' input_bam &&
-        ln -s '$input.metadata.bam_index' input_bam.bai &&
+        ln -sf '$input' input_bam &&
+        ln -sf '$input.metadata.bam_index' input_bam.bai &&
         bam2msa
             #if $region_start and $region_end:
                 -r $region_start:$region_end
             #end if
-            'input_bam' '$output'
+            'input_bam'
+            '$output'
         ]]></command>
     <inputs>
         <param name="input" type="data" format="bam,sam" label="Input BAM file"/>
diff -r 359e043a285c -r 27673f5b5343 macros.xml
--- a/macros.xml	Mon Nov 08 11:40:50 2021 +0000
+++ b/macros.xml	Sun Feb 25 19:30:19 2024 +0000
@@ -1,7 +1,8 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.20.4</token>
-    <token name="@PROFILE@">20.05</token>
+    <token name="@TOOL_VERSION@">0.21.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.05</token>
     <token name="@SANITIZE@"><![CDATA[| gawk '{ if (\$0 ~ "^[^>]") {a = gensub(/[^ACGTURYKMSWBDHVNacgturykmswbdhvn?-]/, "", "g"); } else {a=gensub(/[^>A-Za-z0-9_]/, "_", "g"); }; print a } ' | sed 's,_\\+,_,g' >]]></token>
     <xml name="requirements">
         <requirements>
diff -r 359e043a285c -r 27673f5b5343 test-data/bealign-out1.bam
Binary file test-data/bealign-out1.bam has changed
diff -r 359e043a285c -r 27673f5b5343 test-data/bealign-out2.bam
Binary file test-data/bealign-out2.bam has changed
diff -r 359e043a285c -r 27673f5b5343 test-data/bealign-out3-background.bam
Binary file test-data/bealign-out3-background.bam has changed
diff -r 359e043a285c -r 27673f5b5343 test-data/bealign-out3.bam
Binary file test-data/bealign-out3.bam has changed
diff -r 359e043a285c -r 27673f5b5343 test-data/bealign-out4.bam
Binary file test-data/bealign-out4.bam has changed