Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.xml @ 21:f752a90d266f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 2759e9b0ec00022871f493fb43540c5602f74a5a
author drosofff
date Tue, 27 Jun 2017 04:21:44 -0400
parents ffe2430ef56d
children 764181d43c36
comparison
equal deleted inserted replaced
20:ffe2430ef56d 21:f752a90d266f
44 44
45 #set $method_postfix = " %s %s " % ($method_prefix, $extra_output) 45 #set $method_postfix = " %s %s " % ($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_postfix --suppress 6,7,8 $extra_output "local_index" $format $input > $output 49 bowtie -p \${GALAXY_SLOTS:-4} '${method_postfix}' --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_postfix $extra_output -S "local_index" $format $input > $output 51 bowtie -p \${GALAXY_SLOTS:-4} '${method_postfix}' '${extra_output}' -S local_index '${format}' $input > $output
52 #elif $output_format == "bam": 52 #elif $output_format == "bam":
53 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix $extra_output -S "local_index" $format $input |samtools view -bS - > $output 53 bowtie -p \${GALAXY_SLOTS:-4} '${method_postfix}' '${extra_output}' -S local_index '${format}' $input |samtools view -bS - > $output
54 #end if 54 #end if
55 55
56 ]]></command> 56 ]]></command>
57 <inputs> 57 <inputs>
58 <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" /> 58 <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" />