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comparison nanopolish_methylation.xml @ 0:f9dadc362197 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
author bgruening
date Wed, 30 May 2018 11:55:55 -0400
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-1:000000000000 0:f9dadc362197
1 <tool id="nanopolish_methylation" name="Nanopolish methylation" version="0.1.0">
2 <description>- Classify nucleotides as methylated or not.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 ln -s '$input_merged' reads.fasta &&
9
10 #if $input_reads_raw.extension == 'fast5':
11 mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
12 #else
13 ln -s '$input_reads_raw' fast5_files.tar.gz &&
14 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
15 #end if
16
17 nanopolish index -d fast5_files/ reads.fasta &&
18 ln -s '$b' reads.bam &&
19 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
20 ln -s '$g' genome.fa &&
21
22 nanopolish call-methylation
23 -r reads.fasta
24 -b reads.bam
25 -g genome.fa
26 #if $w and str($w).strip():
27 -w "${w}"
28 #end if
29 > methylation_calls.tsv
30 ]]></command>
31 <inputs>
32 <!-- index inputs -->
33 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
34 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/>
35
36 <!-- variants consensus inputs -->
37 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
38 <param type="data" argument="-g" format="fasta" label="The reference genome"/>
39
40 <param argument="-w" type="text" optional="true"
41 label="find variants in window of region chromsome:start-end" />
42
43 </inputs>
44
45 <outputs>
46 <!-- variants consensus outputs -->
47 <data name="output_methylation_calls" format="tabular" from_work_dir="methylation_calls.tsv" label="called methylation sites" />
48 </outputs>
49 <tests>
50 <test>
51 <!-- index test -->
52 <param name="input_merged" ftype="fasta" value="reads.fasta" />
53 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
54
55 <!-- variants consensus test -->
56 <param name="b" value="reads.sorted.bam" />
57 <param name="g" value="draft.fa" />
58 <param name="w" value="tig00000001:200000-202000" />
59
60 <output name="output_methylation_calls" file="methylation_calls.tsv" />
61 </test>
62 </tests>
63 <help><![CDATA[
64 Usage: nanopolish call-methylation [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
65 Classify nucleotides as methylated or not.
66
67 Quickstart tutorial and manual available at:
68 http://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html
69
70 ]]></help>
71 <expand macro="citations" />
72 </tool>