Mercurial > repos > bgruening > nanopolish_methylation

annotate 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
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1 <tool id="nanopolish_methylation" name="Nanopolish methylation" version="0.1.0">
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2 <description>- Classify nucleotides as methylated or not.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 ln -s '$input_merged' reads.fasta &&
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9
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10 #if $input_reads_raw.extension == 'fast5':
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11 mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
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12 #else
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13 ln -s '$input_reads_raw' fast5_files.tar.gz &&
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14 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
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15 #end if
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17 nanopolish index -d fast5_files/ reads.fasta &&
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18 ln -s '$b' reads.bam &&
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19 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
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20 #if $reference_source.reference_source_selector == 'history':
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21 ln -f -s '$reference_source.ref_file' genome.fa &&
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22 #else:
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23 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
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24 #end if
0
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26 nanopolish call-methylation
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27 -r reads.fasta
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28 -b reads.bam
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29 -g genome.fa
1
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30 #if str($batchsize):
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31 -K $batchsize
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32 #end if
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33 --threads "\${GALAXY_SLOTS:-4}"
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34 #if $w and str($w).strip():
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35 -w "${w}"
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36 #end if
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37 > methylation_calls.tsv
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38 ]]></command>
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39 <inputs>
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40 <!-- index inputs -->
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41 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
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42 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/>
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43
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44 <!-- variants consensus inputs -->
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45 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
1
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46 <conditional name="reference_source">
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47 <param name="reference_source_selector" type="select" label="Load reference genome from">
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48 <option value="cached">Local cache</option>
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49 <option value="history">History</option>
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50 </param>
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51 <when value="cached">
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52 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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53 <options from_data_table="all_fasta">
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54 </options>
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55 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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56 </param>
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57 </when>
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58 <when value="history">
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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" />
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60 </when>
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61 </conditional>
0
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62 <param argument="-w" type="text" optional="true"
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63 label="find variants in window of region chromsome:start-end" />
1
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64 <param name="batchsize" type="integer" optional="true" value="" label="Batch size" help="(-K)"/>
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65
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66 </inputs>
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67
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68 <outputs>
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69 <!-- variants consensus outputs -->
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70 <data name="output_methylation_calls" format="tabular" from_work_dir="methylation_calls.tsv" label="called methylation sites" />
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71 </outputs>
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72 <tests>
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73 <test>
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74 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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75 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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76 <param name="b" value="reads.sorted.bam" />
1
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77 <param name="reference_source_selector" value="history" />
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78 <param name="ref_file" value="draft.fa" />
0
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79 <param name="w" value="tig00000001:200000-202000" />
1
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80 <param name="batchsize" value="512" />
0
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81 <output name="output_methylation_calls" file="methylation_calls.tsv" />
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82 </test>
1
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83 <test>
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84 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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85 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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86 <param name="reference_source_selector" value="cached" />
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87 <param name="ref_file" value="draft"/>
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88 <param name="b" value="reads.sorted.bam" />
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89 <param name="w" value="tig00000001:200000-202000" />
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90 <param name="batchsize" value="512" />
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91 <output name="output_methylation_calls" file="methylation_calls.tsv" />
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92 </test>
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93 </tests>
0
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94 <help><![CDATA[
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95 Usage: nanopolish call-methylation [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
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96 Classify nucleotides as methylated or not.
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97
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98 Quickstart tutorial and manual available at:
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99 http://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html
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100
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101 ]]></help>
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102 <expand macro="citations" />
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103 </tool>