Mercurial > repos > devteam > sam_to_bam

diff sam_to_bam.xml @ 9:d83ad701f011 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
author iuc
date Sat, 27 Nov 2021 12:27:56 +0000
parents c701f5f96f32
children
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line diff
--- a/sam_to_bam.xml	Tue Sep 28 15:58:15 2021 +0000
+++ b/sam_to_bam.xml	Sat Nov 27 12:27:56 2021 +0000
@@ -16,7 +16,7 @@
         samtools view
             -b
             -@ \$addthreads
-            -t '$reffai'
+            -t "\$reffai"
             '$input' |
 
         samtools sort
@@ -67,6 +67,20 @@
             <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
             <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
         </test>
+        <test>
+            <!-- Test direct use of bgzipped reference -->
+            <param name="addref_select" value="history" />
+            <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" />
+            <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
+            <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
+        </test>
+        <test>
+            <!-- Test with simple gzipped reference, which requires decompression -->
+            <param name="addref_select" value="history" />
+            <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" />
+            <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
+            <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**