Mercurial > repos > bgruening > nanopolish_methylation

annotate nanopolish_methylation.xml @ 8:90a922f32523 draft default tip

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author bgruening
date Thu, 30 Nov 2023 17:58:25 +0000
parents 12efe2f03697
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1 <tool id="nanopolish_methylation" name="Nanopolish methylation" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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[
8
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8 @PREPROCESS_INPUTS@
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10 nanopolish call-methylation
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11 -r reads.fasta
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12 -b reads.bam
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13 -g genome.fa
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14 #if str($batchsize):
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15 -K $batchsize
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16 #end if
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17 --threads "\${GALAXY_SLOTS:-4}"
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18 #if $w and str($w).strip():
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19 -w "${w}"
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20 #end if
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21 > methylation_calls.tsv
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22 ]]></command>
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23 <inputs>
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24 <!-- index inputs -->
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25 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
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26 <param type="data" name="input_reads_raw" format="fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
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27
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28 <!-- variants consensus inputs -->
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29 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
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30 <conditional name="reference_source">
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31 <param name="reference_source_selector" type="select" label="Load reference genome from">
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32 <option value="cached">Local cache</option>
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33 <option value="history">History</option>
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34 </param>
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35 <when value="cached">
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36 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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37 <options from_data_table="all_fasta">
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38 </options>
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39 <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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40 </param>
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41 </when>
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42 <when value="history">
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43 <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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44 </when>
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45 </conditional>
3
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46
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47 <section name="adv" title="Optional data inputs">
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48 <!-- optional inputs -->
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49 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/>
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50 </section>
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51
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52 <param argument="-w" type="text" optional="true"
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53 label="find variants in window of region chromsome:start-end" />
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54 <param name="batchsize" type="integer" optional="true" value="" label="Batch size" help="(-K)"/>
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55
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56 </inputs>
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57
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58 <outputs>
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59 <!-- variants consensus outputs -->
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60 <data name="output_methylation_calls" format="tabular" from_work_dir="methylation_calls.tsv" label="called methylation sites" />
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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65 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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66 <param name="b" value="reads.sorted.bam" />
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67 <param name="reference_source_selector" value="history" />
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68 <param name="ref_file" value="draft.fa" />
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69 <param name="w" value="tig00000001:200000-202000" />
1
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70 <param name="batchsize" value="512" />
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71 <output name="output_methylation_calls" file="methylation_calls.tsv" />
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72 </test>
1
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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="reference_source_selector" value="history" />
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77 <param name="ref_file" value="draft.fa"/>
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78 <param name="b" value="reads.sorted.bam" />
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79 <param name="w" value="tig00000001:200000-202000" />
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80 <param name="batchsize" value="512" />
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81 <output name="output_methylation_calls" file="methylation_calls.tsv" />
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82 </test>
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83 </tests>
0
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84 <help><![CDATA[
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85 Usage: nanopolish call-methylation [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
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86 Classify nucleotides as methylated or not.
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87
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88 Quickstart tutorial and manual available at:
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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89 http://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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90
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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91 ]]></help>
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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92 <expand macro="citations" />
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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93 </tool>