Mercurial > repos > mvdbeek > bam_readtagger
comparison findcluster.xml @ 35:02afdbc69591 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e4cd04d8a19b57d6b23da64c3fda8978b51e33ef
| author | mvdbeek |
|---|---|
| date | Thu, 14 Dec 2017 03:52:04 -0500 |
| parents | 240c901dedc0 |
| children | d0b3329a8e4b |
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| 34:240c901dedc0 | 35:02afdbc69591 |
|---|---|
| 1 <tool id="findcluster" name="Find clusters of reads" version="0.4.1"> | 1 <tool id="findcluster" name="Find clusters of reads" version="0.4.4"> |
| 2 <description>in bam files</description> | 2 <description>in bam files</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <requirements> | 6 <requirements> |
| 7 <requirement type="package" version="0.4.1">readtagger</requirement> | 7 <requirement type="package" version="0.4.4">readtagger</requirement> |
| 8 </requirements> | 8 </requirements> |
| 9 <version_command>findcluster --version</version_command> | 9 <version_command>findcluster --version</version_command> |
| 10 <command detect_errors="aggressive"><![CDATA[ | 10 <command detect_errors="aggressive"><![CDATA[ |
| 11 #import re | 11 #import re |
| 12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier)) | 12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier)) |
| 16 --input_path input.bam | 16 --input_path input.bam |
| 17 #if $transposon_source.ref_file: | 17 #if $transposon_source.ref_file: |
| 18 #if str($transposon_source.reference_source_selector) == "history": | 18 #if str($transposon_source.reference_source_selector) == "history": |
| 19 --transposon_reference_fasta '$transposon_source.ref_file' | 19 --transposon_reference_fasta '$transposon_source.ref_file' |
| 20 #else : | 20 #else : |
| 21 --transposon_bwa_index '$reference_source.ref_file.fields.path' | 21 --transposon_bwa_index '$transposon_source.ref_file.fields.path' |
| 22 #end if | 22 #end if |
| 23 #end if | 23 #end if |
| 24 #if $genome_source.ref_file: | 24 #if $genome_source.ref_file: |
| 25 #if str($genome_source.reference_source_selector) == "history": | 25 #if str($genome_source.reference_source_selector) == "history": |
| 26 --genome_reference_fasta '$genome_source.ref_file' | 26 --genome_reference_fasta '$genome_source.ref_file' |
| 27 #else : | 27 #else : |
| 28 --genome_bwa_index '$reference_source.ref_file.fields.path' | 28 --genome_bwa_index '$genome_source.ref_file.fields.path' |
| 29 #end if | 29 #end if |
| 30 #end if | 30 #end if |
| 31 --output_bam '$output_bam' | 31 --output_bam '$output_bam' |
| 32 --output_gff '$output_gff' | 32 --output_gff '$output_gff' |
| 33 --output_fasta '$output_fasta' | 33 --output_fasta '$output_fasta' |