changeset 8:27673f5b5343 draft

planemo upload for repository https://github.com/davebx/bioext-gx/ commit 473fd4bfc9bc6dc149978013545525529978b988
author iuc
date Sun, 25 Feb 2024 19:30:19 +0000
parents 359e043a285c
children 7ecb45126cd2
files bam2msa.xml macros.xml test-data/bealign-out1.bam test-data/bealign-out2.bam test-data/bealign-out3-background.bam test-data/bealign-out3.bam test-data/bealign-out4.bam
diffstat 7 files changed, 7 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- 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"/>
--- 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>
Binary file test-data/bealign-out1.bam has changed
Binary file test-data/bealign-out2.bam has changed
Binary file test-data/bealign-out3-background.bam has changed
Binary file test-data/bealign-out3.bam has changed
Binary file test-data/bealign-out4.bam has changed