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comparison sRbowtie.xml @ 29:04685a1b3de1 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 12:34:18 -0400
parents c1ae0c9ad7d1
children 5bd8c555390d
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28:c1ae0c9ad7d1 29:04685a1b3de1
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2">bowtie</requirement> 4 <requirement type="package" version="1.2">bowtie</requirement>
5 <requirement type="package" version="1.4.1">samtools</requirement> 5 <requirement type="package" version="1.4.1">samtools</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #if str($refGenomeSource.genomeSource) == "history": 8 #if $refGenomeSource.genomeSource == "history":
9 bowtie-build -f $refGenomeSource.ownFile local_index && 9 bowtie-build -f $refGenomeSource.ownFile local_index &&
10 #else: 10 #else:
11 ln -f -s $refGenomeSource.index.fields.path local_index && 11 ln -f -s $refGenomeSource.index.fields.path local_index &&
12 #end if 12 #end if
13 #if $input.extension == "fasta": 13 #if $input.extension == "fasta":
43 #end if 43 #end if
44 44
45 #set $method_postfix = " %s %s " % ($method_prefix, $extra_output) 45 #set $method_postfix = " %s %s " % ($method_prefix, $extra_output)
46 46
47 ## run the bowtie alignement 47 ## run the bowtie alignement
48 #if str($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' > '$output'
50 #elif str($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' > '$output'
52 #elif str($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>