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comparison nanopolish_methylation.xml @ 8:90a922f32523 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
author bgruening
date Thu, 30 Nov 2023 17:58:25 +0000
parents 12efe2f03697
children
comparison
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7:be95355fef8d 8:90a922f32523
1 <tool id="nanopolish_methylation" name="Nanopolish methylation" version="@VERSION@+galaxy0"> 1 <tool id="nanopolish_methylation" name="Nanopolish methylation" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>- Classify nucleotides as methylated or not.</description> 2 <description>- Classify nucleotides as methylated or not.</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 ln -s '$input_merged' reads.fasta && 8 @PREPROCESS_INPUTS@
9
10 #if $input_reads_raw.extension == 'fast5':
11 mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
12
13 #else if $input_reads_raw.extension == 'fast5.tar':
14 ln -s '$input_reads_raw' fast5_files.tar &&
15 mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files &&
16
17 #else if $input_reads_raw.extension == 'fast5.tar.bz2':
18 ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
19 mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files &&
20
21 #else:
22 ln -s '$input_reads_raw' fast5_files.tar.gz &&
23 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
24
25 #end if
26
27 nanopolish index
28 -d fast5_files/
29 #if $adv.input_seq_summary:
30 -s '$adv.input_seq_summary'
31 #end if
32 reads.fasta &&
33
34 ln -s '$b' reads.bam &&
35 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
36 #if $reference_source.reference_source_selector == 'history':
37 ln -f -s '$reference_source.ref_file' genome.fa &&
38 #else:
39 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
40 #end if
41 9
42 nanopolish call-methylation 10 nanopolish call-methylation
43 -r reads.fasta 11 -r reads.fasta
44 -b reads.bam 12 -b reads.bam
45 -g genome.fa 13 -g genome.fa
46 #if str($batchsize): 14 #if str($batchsize):
47 -K $batchsize 15 -K $batchsize
48 #end if 16 #end if
49 --threads "\${GALAXY_SLOTS:-4}" 17 --threads "\${GALAXY_SLOTS:-4}"
50 #if $w and str($w).strip(): 18 #if $w and str($w).strip():
51 -w "${w}" 19 -w "${w}"
52 #end if 20 #end if
53 > methylation_calls.tsv 21 > methylation_calls.tsv
54 ]]></command> 22 ]]></command>
55 <inputs> 23 <inputs>
56 <!-- index inputs --> 24 <!-- index inputs -->
57 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> 25 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>