Mercurial > repos > iuc > bwameth
diff bwameth.xml @ 6:b4e6819b25ef draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 6d44811a45b4f6fded1ec72450ed300318095ce4"
| author | iuc |
|---|---|
| date | Tue, 13 Jul 2021 13:56:29 +0000 |
| parents | 29bdbc353f20 |
| children | 6da3972210ee |
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--- a/bwameth.xml Tue Oct 01 17:53:32 2019 -0400 +++ b/bwameth.xml Tue Jul 13 13:56:29 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="bwameth" name="bwameth" version="@TOOL_VERSION@" profile="17.01"> +<tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy1" profile="20.05"> <description>Fast and accurate aligner of BS-Seq reads.</description> <macros> <token name="@TOOL_VERSION@">0.2.2</token> @@ -78,7 +78,7 @@ #else: $read1 $read2 #end if -| samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam - +| samtools view --no-PG -u - | samtools sort --no-PG -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam - ]]></command> <inputs> <conditional name="referenceSource"> @@ -130,7 +130,7 @@ <param name="single_or_paired_opts" value="paired" /> <param name="input_mate1" value="t_R1.fastq.gz"/> <param name="input_mate2" value="t_R2.fastq.gz"/> - <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> + <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff--> </test> <test> <param name="referenceSource" value="history" /> @@ -142,7 +142,7 @@ <element name="reverse" value="t_R2.fastq.gz"/> </collection> </param> - <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> + <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff--> </test> </tests> <help><![CDATA[