# HG changeset patch
# User iuc
# Date 1627716379 0
# Node ID 858ada516d8f0019694108b86e118669dcd8e280
# Parent  a744bb7196a2db7ea77971b6ea2be2abb4021f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 9aed35e37c5bc8ee17a02930c1f2edceb8b0d97b"

diff -r a744bb7196a2 -r 858ada516d8f macros.xml
--- a/macros.xml	Thu Oct 17 02:17:06 2019 -0400
+++ b/macros.xml	Sat Jul 31 07:26:19 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 a744bb7196a2 -r 858ada516d8f samtools_cram_to_bam.xml
--- 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