Mercurial > repos > bgruening > nanopolish_methylation

comparison nanopolish_methylation.xml @ 3:02e3c674d917 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
author bgruening
date Wed, 19 Jun 2019 03:45:24 -0400
parents 709490665bad
children a8d4be409446
comparison
equal deleted inserted replaced
2:07cf146e8964 3:02e3c674d917
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 ln -s '$input_merged' reads.fasta && 8 ln -s '$input_merged' reads.fasta &&
9 9
10 #if $input_reads_raw.extension == 'fast5': 10 #if $input_reads_raw.extension == 'fast5':
11 mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 && 11 mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
12 #else 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:
13 ln -s '$input_reads_raw' fast5_files.tar.gz && 22 ln -s '$input_reads_raw' fast5_files.tar.gz &&
14 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files && 23 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
24
15 #end if 25 #end if
16 26
17 nanopolish index -d fast5_files/ reads.fasta && 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
18 ln -s '$b' reads.bam && 34 ln -s '$b' reads.bam &&
19 ln -s '${b.metadata.bam_index}' reads.bam.bai && 35 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
20 #if $reference_source.reference_source_selector == 'history': 36 #if $reference_source.reference_source_selector == 'history':
21 ln -f -s '$reference_source.ref_file' genome.fa && 37 ln -f -s '$reference_source.ref_file' genome.fa &&
22 #else: 38 #else:
37 > methylation_calls.tsv 53 > methylation_calls.tsv
38 ]]></command> 54 ]]></command>
39 <inputs> 55 <inputs>
40 <!-- index inputs --> 56 <!-- index inputs -->
41 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> 57 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
42 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/> 58 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
43 59
44 <!-- variants consensus inputs --> 60 <!-- variants consensus inputs -->
45 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> 61 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
46 <conditional name="reference_source"> 62 <conditional name="reference_source">
47 <param name="reference_source_selector" type="select" label="Load reference genome from"> 63 <param name="reference_source_selector" type="select" label="Load reference genome from">
57 </when> 73 </when>
58 <when value="history"> 74 <when value="history">
59 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> 75 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
60 </when> 76 </when>
61 </conditional> 77 </conditional>
78
79 <section name="adv" title="Optional data inputs">
80 <!-- optional inputs -->
81 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/>
82 </section>
83
62 <param argument="-w" type="text" optional="true" 84 <param argument="-w" type="text" optional="true"
63 label="find variants in window of region chromsome:start-end" /> 85 label="find variants in window of region chromsome:start-end" />
64 <param name="batchsize" type="integer" optional="true" value="" label="Batch size" help="(-K)"/> 86 <param name="batchsize" type="integer" optional="true" value="" label="Batch size" help="(-K)"/>
65 87
66 </inputs> 88 </inputs>