diff samtools_cram_to_bam.xml @ 3:858ada516d8f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 9aed35e37c5bc8ee17a02930c1f2edceb8b0d97b"

--- a/samtools_cram_to_bam.xml	Thu Oct 17 02:17:06 2019 -0400
+++ b/samtools_cram_to_bam.xml	Sat Jul 31 07:26:19 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@">
+<tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@+galaxy1">
     <description>convert CRAM alignments to BAM format</description>
 
     <macros>
@@ -9,8 +9,10 @@
     <expand macro="version_command"/>
 
     <command><![CDATA[
+        #set input_cram = "input.cram"
+        ln -s '${input_alignment}' '${input_cram}' &&
         #if str( $input_alignment.metadata.cram_index ) != "None":
-            ln -f -s '${input_alignment.metadata.cram_index}' '${input_alignment}.crai' &&
+            ln -f -s '${input_alignment.metadata.cram_index}' '${input_cram}.crai' &&
         #end if
 
         #if $reference_source.reference_source_selector == 'history':
@@ -28,7 +30,7 @@
             -b
             -T '$ref_fa'
             -o '$output_alignment'
-            '$input_alignment'
+            '$input_cram'
             #if $parameter_regions.target_region == "region"
                 '${parameter_regions.region_string}'
             #end if