diff bam_to_sam.xml @ 3:c1419fa820c6 draft

Uploaded

--- a/bam_to_sam.xml	Thu Mar 05 21:22:11 2015 -0500
+++ b/bam_to_sam.xml	Wed Mar 18 15:44:51 2015 -0400
@@ -1,63 +1,50 @@
-<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.4">
-  <requirements>
-    <requirement type="package" version="0.1.19">samtools</requirement>
-  </requirements>
-  <description>converts BAM format to SAM format</description>
-  <command interpreter="python">
-    bam_to_sam.py
-      --input1=$input1
-      --output1=$output1
-      $header
-  </command>
-  <inputs>
-    <param name="input1" type="data" format="bam" label="BAM File to Convert" />
-    <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" />
-  </inputs>
-  <outputs>
-    <data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" />
-  </outputs>
-  <tests>
-    <test>
-      <!--
-      Bam-to-Sam command:
-      samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam
-      bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
-      -->
-      <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
-      <param name="header" value="" />
-      <output name="output1" file="bam_to_sam_out1.sam" sorted="True" />
-    </test>
-    <test>
-      <!--
-      Bam-to-Sam command:
-      samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam
-      bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam
-      -->
-      <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" />
-      <param name="header" value="" />
-      <output name="output1" file="bam_to_sam_out2.sam" sorted="True" />
-    </test>
-    <test>
-      <!--
-      Bam-to-Sam command:
-      samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam
-      bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
-      -->
-      <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
-      <param name="header" value="--header" />
-      <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) -->
-    </test>
-  </tests>
-  <help>
+<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.6">
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="version_command"></expand>
+  <expand macro="stdio"></expand>
+  <description>converts BAM format to SAM format</description>  
+    <command>
+<![CDATA[
+  samtools sort -O bam -@ \${GALAXY_SLOTS:-1} "$input1" -o sorted_input.bam -T temp && 
+  samtools view sorted_input.bam $header -o $output1 -@ \${GALAXY_SLOTS:-1}
+]]>
+    </command>
+    <inputs>
+        <param format="bam" label="BAM File to Convert" name="input1" type="data" />
+        <param checked="False" falsevalue="" label="Include header in output" name="header" truevalue="-h" type="boolean" />
+    </inputs>
+    <outputs>
+        <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
+    </outputs>
+    <tests>
+        <test>
+            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
+            <param name="header" value="" />
+            <output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
+        </test>
+        <test>
+            <param ftype="bam" name="input1" value="bam_to_sam_in2.bam" />
+            <param name="header" value="" />
+            <output file="bam_to_sam_out2.sam" name="output1" sorted="True" />
+        </test>
+        <test>
+            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
+            <param name="header" value="True" />
+            <output file="bam_to_sam_out3.sam" name="output1" sorted="True" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
 
 **What it does**
 
 This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file.
 
 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
-
+]]>
   </help>
-  <citations>
-      <citation type="doi">10.1093/bioinformatics/btp352</citation>
-  </citations>
+  <expand macro="citations"></expand>
 </tool>