Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.xml @ 18:9fe34d55bfb0 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 083e56a5896485479dfd679e0b571eb2bd8aed0b
author drosofff
date Mon, 26 Jun 2017 19:49:25 -0400
parents 0806b5d0b5da
children dd5985c5798d
comparison
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17:0806b5d0b5da 18:9fe34d55bfb0
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #if $refGenomeSource.genomeSource == "history": 8 #if $refGenomeSource.genomeSource == "history":
9 bowtie-build -f '$refGenomeSource.ownFile' local_index && 9 bowtie-build -f '$refGenomeSource.ownFile' local_index &&
10 #else: 10 #else:
11 ln -s local_index '$refGenomeSource.index.fields.path' && 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":
14 #set format = "-f" 14 #set format = "-f"
15 #elif $input.extension == "fastq": 15 #elif $input.extension == "fastq":
16 #set format = "-q" 16 #set format = "-q"
40 #set extra_output = " --un %s " % str($unaligned) 40 #set extra_output = " --un %s " % str($unaligned)
41 #else: 41 #else:
42 #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned)) 42 #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned))
43 #end if 43 #end if
44 44
45 #set $method_postfix = "$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_prefix --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_prefix $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_prefix $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" />