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 |
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date | Thu, 14 Dec 2017 03:52:04 -0500 |
parents | 240c901dedc0 |
children | d0b3329a8e4b |
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34:240c901dedc0 | 35:02afdbc69591 |
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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' |