Mercurial > repos > artbio > sr_bowtie
comparison sRbowtie.xml @ 1:5f4fbba31b6a draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 2dac5b5f1ed589f4c8a3c6d64696b842ece8edd2
| author | artbio |
|---|---|
| date | Wed, 11 Oct 2017 06:01:15 -0400 |
| parents | de9cd3998571 |
| children | 304adcfe3660 |
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| 0:de9cd3998571 | 1:5f4fbba31b6a |
|---|---|
| 1 <tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.0"> | 1 <tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.1"> |
| 2 <description>for small RNA short reads</description> | 2 <description>for small RNA short reads</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.1.2=py27_2">bowtie</requirement> | 4 <requirement type="package" version="1.1.2=py27_2">bowtie</requirement> |
| 5 <requirement type="package" version="1.2">samtools</requirement> | 5 <requirement type="package" version="1.2">samtools</requirement> |
| 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 genome && | 9 bowtie-build -f $refGenomeSource.ownFile genome 1>/dev/null && |
| 10 ln -s -f '$refGenomeSource.ownFile' genome.fa && | 10 ln -s -f '$refGenomeSource.ownFile' genome.fa && |
| 11 #set index_path = 'genome' | 11 #set index_path = 'genome' |
| 12 #else: | 12 #else: |
| 13 #set index_path = $refGenomeSource.index.fields.path | 13 #set index_path = $refGenomeSource.index.fields.path |
| 14 #end if | 14 #end if |
| 46 | 46 |
| 47 #set $method_postfix = " %s %s " % ($method_prefix, $extra_output) | 47 #set $method_postfix = " %s %s " % ($method_prefix, $extra_output) |
| 48 | 48 |
| 49 ## run the bowtie alignement | 49 ## run the bowtie alignement |
| 50 #if $output_format == "tabular": | 50 #if $output_format == "tabular": |
| 51 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $index_path $format '$input' > $output | 51 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $index_path $format '$input' 2>&1 > $output |
| 52 #elif $output_format == "sam": | 52 #elif $output_format == "sam": |
| 53 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' > '$output' | 53 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' 2>&1 > '$output' |
| 54 #elif $output_format == "bam": | 54 #elif $output_format == "bam": |
| 55 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output | 55 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input'| samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output 2>&1 |
| 56 #end if | 56 #end if |
| 57 ##### | samtools view -uS | 57 ##### | samtools view -uS |
| 58 ]]></command> | 58 ]]></command> |
| 59 <inputs> | 59 <inputs> |
| 60 <param format="fasta, fastq" help="Only with clipped, fasta or fastq read files" label="Input fasta or fastq file: reads clipped from their adapter" name="input" type="data" /> | 60 <param format="fasta, fastq" help="Only with clipped, fasta or fastq read files" label="Input fasta or fastq file: reads clipped from their adapter" name="input" type="data" /> |