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comparison nanopolish_methylation.xml @ 1:709490665bad draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
author bgruening
date Tue, 05 Jun 2018 17:56:11 -0400
parents f9dadc362197
children 02e3c674d917
comparison
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0:f9dadc362197 1:709490665bad
15 #end if 15 #end if
16 16
17 nanopolish index -d fast5_files/ reads.fasta && 17 nanopolish index -d fast5_files/ reads.fasta &&
18 ln -s '$b' reads.bam && 18 ln -s '$b' reads.bam &&
19 ln -s '${b.metadata.bam_index}' reads.bam.bai && 19 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
20 ln -s '$g' genome.fa && 20 #if $reference_source.reference_source_selector == 'history':
21 ln -f -s '$reference_source.ref_file' genome.fa &&
22 #else:
23 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
24 #end if
21 25
22 nanopolish call-methylation 26 nanopolish call-methylation
23 -r reads.fasta 27 -r reads.fasta
24 -b reads.bam 28 -b reads.bam
25 -g genome.fa 29 -g genome.fa
30 #if str($batchsize):
31 -K $batchsize
32 #end if
33 --threads "\${GALAXY_SLOTS:-4}"
26 #if $w and str($w).strip(): 34 #if $w and str($w).strip():
27 -w "${w}" 35 -w "${w}"
28 #end if 36 #end if
29 > methylation_calls.tsv 37 > methylation_calls.tsv
30 ]]></command> 38 ]]></command>
33 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> 41 <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"/> 42 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/>
35 43
36 <!-- variants consensus inputs --> 44 <!-- variants consensus inputs -->
37 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> 45 <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"/> 46 <conditional name="reference_source">
39 47 <param name="reference_source_selector" type="select" label="Load reference genome from">
48 <option value="cached">Local cache</option>
49 <option value="history">History</option>
50 </param>
51 <when value="cached">
52 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
53 <options from_data_table="all_fasta">
54 </options>
55 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
56 </param>
57 </when>
58 <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" />
60 </when>
61 </conditional>
40 <param argument="-w" type="text" optional="true" 62 <param argument="-w" type="text" optional="true"
41 label="find variants in window of region chromsome:start-end" /> 63 label="find variants in window of region chromsome:start-end" />
64 <param name="batchsize" type="integer" optional="true" value="" label="Batch size" help="(-K)"/>
42 65
43 </inputs> 66 </inputs>
44 67
45 <outputs> 68 <outputs>
46 <!-- variants consensus outputs --> 69 <!-- variants consensus outputs -->
47 <data name="output_methylation_calls" format="tabular" from_work_dir="methylation_calls.tsv" label="called methylation sites" /> 70 <data name="output_methylation_calls" format="tabular" from_work_dir="methylation_calls.tsv" label="called methylation sites" />
48 </outputs> 71 </outputs>
49 <tests> 72 <tests>
50 <test> 73 <test>
51 <!-- index test -->
52 <param name="input_merged" ftype="fasta" value="reads.fasta" /> 74 <param name="input_merged" ftype="fasta" value="reads.fasta" />
53 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> 75 <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" /> 76 <param name="b" value="reads.sorted.bam" />
57 <param name="g" value="draft.fa" /> 77 <param name="reference_source_selector" value="history" />
78 <param name="ref_file" value="draft.fa" />
58 <param name="w" value="tig00000001:200000-202000" /> 79 <param name="w" value="tig00000001:200000-202000" />
59 80 <param name="batchsize" value="512" />
60 <output name="output_methylation_calls" file="methylation_calls.tsv" /> 81 <output name="output_methylation_calls" file="methylation_calls.tsv" />
61 </test> 82 </test>
62 </tests> 83 <test>
84 <param name="input_merged" ftype="fasta" value="reads.fasta" />
85 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
86 <param name="reference_source_selector" value="cached" />
87 <param name="ref_file" value="draft"/>
88 <param name="b" value="reads.sorted.bam" />
89 <param name="w" value="tig00000001:200000-202000" />
90 <param name="batchsize" value="512" />
91 <output name="output_methylation_calls" file="methylation_calls.tsv" />
92 </test>
93 </tests>
63 <help><![CDATA[ 94 <help><![CDATA[
64 Usage: nanopolish call-methylation [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa 95 Usage: nanopolish call-methylation [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
65 Classify nucleotides as methylated or not. 96 Classify nucleotides as methylated or not.
66 97
67 Quickstart tutorial and manual available at: 98 Quickstart tutorial and manual available at: