Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.xml @ 15:44d61fa7fb75 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 52409b39598052ed0eae765a8a9e277c82611e8d
author drosofff
date Mon, 26 Jun 2017 15:18:23 -0400
parents a05b107fd0c4
children 57b6452f9d76
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14:a05b107fd0c4 15:44d61fa7fb75
33 33
34 ## set the extra_output 34 ## set the extra_output
35 #if $additional_fasta == "No": 35 #if $additional_fasta == "No":
36 #set extra_output = "" 36 #set extra_output = ""
37 #elif $additional_fasta == "al": 37 #elif $additional_fasta == "al":
38 #set extra_output = " --un %s" % str(unaligned) 38 #set extra_output = " --al %s " % str($aligned)
39 #elif $additional_fasta == "unal":
40 #set extra_output = " --un %s " % str($unaligned)
39 #else: 41 #else:
40 #set extra_output = " --al %s --un %s" % (str($aligned), str(unaligned)) 42 #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned))
41 #end if 43 #end if
42 44
43 #set $method_postfix = "$method_prefix" + "$extra_output" 45 #set $method_postfix = "$method_prefix" + "$extra_output"
44 46
45 ## run the bowtie alignement 47 ## run the bowtie alignement
46 #if $output_format == "tabular": 48 #if $output_format == "tabular":
47 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix --suppress 6,7,8 "local_index" $format $input > $output 49 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix --suppress 6,7,8 $extra_output$"local_index" $format $input > $output
48 #elif $output_format == "sam": 50 #elif $output_format == "sam":
49 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix -S "local_index" $format $input > $output 51 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix $extra_output -S "local_index" $format $input > $output
50 #elif $output_format == "bam": 52 #elif $output_format == "bam":
51 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix -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
52 #end if 54 #end if
53 55
54 ]]></command> 56 ]]></command>
55 <inputs> 57 <inputs>
56 <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" />