diff sam_to_bam.xml @ 7:881e16ad05c6 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/sam_to_bam commit a1517c9d22029095120643bbe2c8fa53754dd2b7

--- a/sam_to_bam.xml	Tue Apr 21 14:52:20 2015 -0400
+++ b/sam_to_bam.xml	Wed Nov 11 12:51:52 2015 -0500
@@ -1,22 +1,21 @@
-<tool id="sam_to_bam" name="SAM-to-BAM" version="2.0">
+<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1">
   <description>convert SAM to BAM</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"></expand>
+  <expand macro="stdio"></expand>
   <expand macro="version_command"></expand>
-  <expand macro="stdio"></expand>
   <command>
     <![CDATA[
-        samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o sorted_input.bam -T temp "$input1" && 
-          #if $source.index_source == "history":
-            ln -s $source.ref_file input.fa &&
-            samtools faidx input.fa &&
-          #else
-            ln -s ${source.index.fields.path} input.fa &&
-            ln -s ${source.index.fields.path}.fai input.fa.fai &&
-          #end if
-          samtools view -@ \${GALAXY_SLOTS:-1} -b -h -o $output1 -T input.fa sorted_input.bam
+        #if $source.index_source == "history":
+          ln -s $source.ref_file input.fa &&
+          samtools faidx input.fa &&
+        #else
+          ln -s ${source.index.fields.path} input.fa &&
+          ln -s ${source.index.fields.path}.fai input.fa.fai &&
+        #end if
+        samtools view -b -@ \${GALAXY_SLOTS:-1} -t input.fa.fai "$input1" | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o "$output1" -T temp
     ]]>
     </command>
     <inputs>
@@ -68,6 +67,12 @@
             <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
             <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" />
         </test>
+        <test>
+            <param name="index_source" value="history" />
+            <param name="input1" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
+            <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
+            <output file="sam_to_bam_out3.bam" ftype="bam" name="output1" />
+        </test>
     </tests>
     <help>
 <![CDATA[