Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.xml @ 30:5bd8c555390d draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty
author drosofff
date Sun, 02 Jul 2017 12:40:56 -0400
parents 04685a1b3de1
children e0a3a72719f3
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29:04685a1b3de1 30:5bd8c555390d
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 local_index $format '$input' > '$output' 49 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > $output
50 #elif $output_format == "sam": 50 #elif $output_format == "sam":
51 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output' 51 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output'
52 #elif $output_format == "bam": 52 #elif $output_format == "bam":
53 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools sort -O bam -o '$output' 53 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools sort -O bam -o $output
54 #end if 54 #end if
55 ##### | samtools view -uS 55 ##### | samtools view -uS
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" />