Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.xml @ 24:2f4e22f2177d draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit cc96644a48fed1476e854fb7116b5f51c42f9f17
author drosofff
date Wed, 28 Jun 2017 17:45:25 -0400
parents 411b6453b5d0
children 592eab0f31ac
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23:411b6453b5d0 24:2f4e22f2177d
1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.2"> 1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.2">
2 <description>for FASTA small reads</description> 2 <description>for FASTA small reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.2">bowtie</requirement> 4 <requirement type="package" version="1.2">bowtie</requirement>
5 <requirement type="package" version="1.2">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($refGenomeSource.genomeSource) == "history": 8 #if str($refGenomeSource.genomeSource) == "history":
9 bowtie-build -f '$refGenomeSource.ownFile' local_index && 9 bowtie-build -f '$refGenomeSource.ownFile' local_index &&
10 #else: 10 #else:
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' $input | samtools sort -O bam -o '$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" />