diff picard_SamToFastq.xml @ 32:f9242e01365a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309

--- a/picard_SamToFastq.xml	Sat Feb 25 20:33:49 2023 +0000
+++ b/picard_SamToFastq.xml	Mon Sep 25 08:32:17 2023 +0000
@@ -55,7 +55,6 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-    @TMPDIR_OPTION@
 
   ]]></command>
   <inputs>
@@ -104,7 +103,7 @@
   </outputs>
 
   <tests>
-    <test>
+    <test expect_num_outputs="5">
       <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
       <param name="single_or_paired" value="pe_interleaved" />
       <param name="re_reverse" value="true"/>
@@ -118,7 +117,7 @@
       <param name="include_non_primary_alignments" value="false"/>
       <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>
     </test>
-    <test>
+    <test expect_num_outputs="5">
       <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
       <param name="single_or_paired" value="pe_sep" />
       <param name="re_reverse" value="true"/>
@@ -134,7 +133,7 @@
       <output name="fq2" file="picard_SamToFastq_2.fq" ftype="fastqsanger"/>
       <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/>
     </test>
-    <test>
+    <test expect_num_outputs="5">
       <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/>
       <param name="single_or_paired" value="se" />
       <param name="re_reverse" value="true"/>
@@ -157,9 +156,8 @@
 
 Extracts read sequences and qualities from the input SAM/BAM dataset and outputs them in Sanger fastq format. In the RE_REVERSE=True mode (default behavior), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM.BAM dataset will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer.
 
------
+.. class:: warningmark
 
-.. class:: warningmark
 
 @dataset_collections@