Mercurial > repos > mvdbeek > bam_readtagger

comparison findcluster.xml @ 35:5aa7745dd6e3 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0291e13a331e921ff4c5c1859c83cd6f3a8f5f5d
author mvdbeek
date Wed, 21 Jun 2017 09:57:31 -0400
parents 5b08a7a4caa9
children e19ff7992765
comparison
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34:5b08a7a4caa9 35:5aa7745dd6e3
14 --input_path input.bam 14 --input_path input.bam
15 #if $transposon_source.ref_file: 15 #if $transposon_source.ref_file:
16 #if str($transposon_source.reference_source_selector) == "history": 16 #if str($transposon_source.reference_source_selector) == "history":
17 --transposon_reference_fasta '$transposon_source.ref_file' 17 --transposon_reference_fasta '$transposon_source.ref_file'
18 #else : 18 #else :
19 --transposon_bwa_index '$reference_source.ref_file.fields.path' 19 --transposon_bwa_index '$transposon_source.ref_file.fields.path'
20 #end if 20 #end if
21 #end if 21 #end if
22 #if $genome_source.ref_file: 22 #if $genome_source.ref_file:
23 #if str($genome_source.reference_source_selector) == "history": 23 #if str($genome_source.reference_source_selector) == "history":
24 --genome_reference_fasta '$genome_source.ref_file' 24 --genome_reference_fasta '$genome_source.ref_file'
25 #else : 25 #else :
26 --genome_bwa_index '$reference_source.ref_file.fields.path' 26 --genome_bwa_index '$genome_source.ref_file.fields.path'
27 #end if 27 #end if
28 #end if 28 #end if
29 --output_bam '$output_bam' 29 --output_bam '$output_bam'
30 --output_gff '$output_gff' 30 --output_gff '$output_gff'
31 --output_fasta '$output_fasta' 31 --output_fasta '$output_fasta'