changeset 20:4f774c1e6049 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 4a306ebd8b7808ce963a69a3b15dd860c1fde585

--- a/bwa-mem.xml	Fri Dec 22 15:03:03 2017 -0500
+++ b/bwa-mem.xml	Thu Feb 01 12:35:35 2018 -0500
@@ -7,8 +7,7 @@
     </macros>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
-    <command>
-<![CDATA[
+    <command><![CDATA[
 @set_reference_fasta_filename@
 
 ## Begin BWA-MEM command line
@@ -107,8 +106,7 @@
 #end if
 
 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output'
-]]>
-    </command>
+    ]]></command>
 
     <inputs>
         <expand macro="reference_source_conditional" />

--- a/bwa.xml	Fri Dec 22 15:03:03 2017 -0500
+++ b/bwa.xml	Thu Feb 01 12:35:35 2018 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="bwa" name="Map with BWA" version="@VERSION@.3">
+<tool id="bwa" name="Map with BWA" version="@VERSION@.4">
     <description>- map short reads (&lt; 100 bp) against reference genome</description>
     <macros>
         <import>read_group_macros.xml</import>
@@ -305,7 +305,7 @@
     </inputs>
     <outputs>
         <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
-            <expand macro="dbKeyActionsBwa"/>
+            <expand macro="dbKeyActionsBwaMem"/>
         </data>
     </outputs>
     <tests>

--- a/bwa_macros.xml	Fri Dec 22 15:03:03 2017 -0500
+++ b/bwa_macros.xml	Thu Feb 01 12:35:35 2018 -0500
@@ -75,15 +75,6 @@
         </conditional>
     </macro>
 
-    <macro name="dbKeyActionsBwa">
-        <expand macro="dbKeyActions">
-            <option type="from_data_table" name="bwa_indexes" column="1" offset="0">
-                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                <filter type="param_value" ref="reference_source.ref_file" column="0"/>
-            </option>
-        </expand>
-    </macro>
-
     <macro name="dbKeyActionsBwaMem">
         <expand macro="dbKeyActions">
             <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0">