Mercurial > repos > bgruening > nanopolish_methylation

annotate nanopolish_methylation.xml @ 5:12efe2f03697 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
author bgruening
date Fri, 29 May 2020 13:30:11 -0400
parents a8d4be409446
children 90a922f32523
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12efe2f03697 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
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1 <tool id="nanopolish_methylation" name="Nanopolish methylation" version="@VERSION@+galaxy0">
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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13 #else if $input_reads_raw.extension == 'fast5.tar':
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14 ln -s '$input_reads_raw' fast5_files.tar &&
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15 mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files &&
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17 #else if $input_reads_raw.extension == 'fast5.tar.bz2':
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18 ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
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19 mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files &&
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20
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21 #else:
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22 ln -s '$input_reads_raw' fast5_files.tar.gz &&
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23 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
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24
0
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25 #end if
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26
3
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27 nanopolish index
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28 -d fast5_files/
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29 #if $adv.input_seq_summary:
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30 -s '$adv.input_seq_summary'
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31 #end if
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32 reads.fasta &&
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33
0
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34 ln -s '$b' reads.bam &&
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35 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
1
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36 #if $reference_source.reference_source_selector == 'history':
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37 ln -f -s '$reference_source.ref_file' genome.fa &&
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38 #else:
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39 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
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40 #end if
0
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41
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42 nanopolish call-methylation
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43 -r reads.fasta
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44 -b reads.bam
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45 -g genome.fa
1
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46 #if str($batchsize):
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47 -K $batchsize
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48 #end if
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49 --threads "\${GALAXY_SLOTS:-4}"
0
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50 #if $w and str($w).strip():
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51 -w "${w}"
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52 #end if
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53 > methylation_calls.tsv
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54 ]]></command>
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55 <inputs>
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56 <!-- index inputs -->
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57 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
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58 <param type="data" name="input_reads_raw" format="fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
0
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59
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60 <!-- variants consensus inputs -->
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61 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
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62 <conditional name="reference_source">
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63 <param name="reference_source_selector" type="select" label="Load reference genome from">
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64 <option value="cached">Local cache</option>
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65 <option value="history">History</option>
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66 </param>
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67 <when value="cached">
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68 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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69 <options from_data_table="all_fasta">
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70 </options>
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71 <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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72 </param>
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73 </when>
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74 <when value="history">
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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" />
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76 </when>
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77 </conditional>
3
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78
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79 <section name="adv" title="Optional data inputs">
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80 <!-- optional inputs -->
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81 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/>
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82 </section>
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83
0
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84 <param argument="-w" type="text" optional="true"
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85 label="find variants in window of region chromsome:start-end" />
1
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86 <param name="batchsize" type="integer" optional="true" value="" label="Batch size" help="(-K)"/>
0
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87
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88 </inputs>
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89
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90 <outputs>
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91 <!-- variants consensus outputs -->
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92 <data name="output_methylation_calls" format="tabular" from_work_dir="methylation_calls.tsv" label="called methylation sites" />
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93 </outputs>
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94 <tests>
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95 <test>
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96 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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97 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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98 <param name="b" value="reads.sorted.bam" />
1
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99 <param name="reference_source_selector" value="history" />
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100 <param name="ref_file" value="draft.fa" />
0
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101 <param name="w" value="tig00000001:200000-202000" />
1
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102 <param name="batchsize" value="512" />
0
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103 <output name="output_methylation_calls" file="methylation_calls.tsv" />
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104 </test>
1
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105 <test>
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106 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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107 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
4
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108 <param name="reference_source_selector" value="history" />
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109 <param name="ref_file" value="draft.fa"/>
1
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110 <param name="b" value="reads.sorted.bam" />
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111 <param name="w" value="tig00000001:200000-202000" />
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112 <param name="batchsize" value="512" />
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113 <output name="output_methylation_calls" file="methylation_calls.tsv" />
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114 </test>
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115 </tests>
0
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116 <help><![CDATA[
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117 Usage: nanopolish call-methylation [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
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118 Classify nucleotides as methylated or not.
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119
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120 Quickstart tutorial and manual available at:
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121 http://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html
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122
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123 ]]></help>
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124 <expand macro="citations" />
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125 </tool>