Mercurial > repos > artbio > sr_bowtie
comparison sRbowtie.xml @ 2:304adcfe3660 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 9700ca1c08ed2cfbca33630892569f3b8acec6fe
| author | artbio |
|---|---|
| date | Wed, 31 Jan 2018 17:55:20 -0500 |
| parents | 5f4fbba31b6a |
| children | 61ab0d4bd187 |
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| 1:5f4fbba31b6a | 2:304adcfe3660 |
|---|---|
| 1 <tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.1"> | 1 <tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.2"> |
| 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_0">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 1>/dev/null && | 9 bowtie-build -f $refGenomeSource.ownFile genome 1>/dev/null && |
| 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 |
| 15 #if $input.extension == "fasta": | 15 #if $input.extension == "fasta": |
| 16 #set format = "-f" | 16 #set format = "-f" |
| 17 #elif $input.extension == "fastq": | 17 #elif $input.extension == "fastq" or $input.extension == "fastqsanger": |
| 18 #set format = "-q" | 18 #set format = "-q" |
| 19 #end if | 19 #end if |
| 20 | 20 |
| 21 ## set the method_prefix | 21 ## set the method_prefix |
| 22 #if $method == "RNA": | 22 #if $method == "RNA": |
| 151 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> | 151 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> |
| 152 </test> | 152 </test> |
| 153 <test> | 153 <test> |
| 154 <param name="genomeSource" value="history" /> | 154 <param name="genomeSource" value="history" /> |
| 155 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> | 155 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> |
| 156 <param name="method" value="unique" /> | |
| 157 <param ftype="fastqsanger" name="input" value="input.fastqsanger" /> | |
| 158 <param name="v_mismatches" value="1" /> | |
| 159 <param name="output_format" value="bam" /> | |
| 160 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> | |
| 161 </test> | |
| 162 <test> | |
| 163 <param name="genomeSource" value="history" /> | |
| 164 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> | |
| 156 <param name="method" value="multiple" /> | 165 <param name="method" value="multiple" /> |
| 157 <param ftype="fasta" name="input" value="input.fa" /> | 166 <param ftype="fasta" name="input" value="input.fa" /> |
| 158 <param name="v_mismatches" value="1" /> | 167 <param name="v_mismatches" value="1" /> |
| 159 <param name="output_format" value="tabular" /> | 168 <param name="output_format" value="tabular" /> |
| 160 <output file="output.tab" ftype="tabular" name="output" /> | 169 <output file="output.tab" ftype="tabular" name="output" /> |