Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.xml @ 17:0806b5d0b5da draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 9f17bd7ad141b24f5bb3c041a059afa1c268b68f
author drosofff
date Mon, 26 Jun 2017 19:37:53 -0400
parents 57b6452f9d76
children 9fe34d55bfb0
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16:57b6452f9d76 17:0806b5d0b5da
44 44
45 #set $method_postfix = "$method_prefix" + "$extra_output" 45 #set $method_postfix = "$method_prefix" + "$extra_output"
46 46
47 ## run the bowtie alignement 47 ## run the bowtie alignement
48 #if $output_format == "tabular": 48 #if $output_format == "tabular":
49 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix --suppress 6,7,8 $extra_output$"local_index" $format $input > $output 49 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix --suppress 6,7,8 $extra_output "local_index" $format $input > $output
50 #elif $output_format == "sam": 50 #elif $output_format == "sam":
51 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix $extra_output -S "local_index" $format $input > $output 51 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix $extra_output -S "local_index" $format $input > $output
52 #elif $output_format == "bam": 52 #elif $output_format == "bam":
53 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix $extra_output -S "local_index" $format $input |samtools view -bS - > $output 53 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix $extra_output -S "local_index" $format $input |samtools view -bS - > $output
54 #end if 54 #end if