Mercurial > repos > bgruening > nanopolish_methylation

annotate nanopolish_methylation.xml @ 0:f9dadc362197 draft

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author bgruening
date Wed, 30 May 2018 11:55:55 -0400
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f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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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 '$input_reads_raw' fast5_files.tar.gz &&
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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14 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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15 #end if
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17 nanopolish index -d fast5_files/ reads.fasta &&
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18 ln -s '$b' reads.bam &&
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19 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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20 ln -s '$g' genome.fa &&
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f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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22 nanopolish call-methylation
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23 -r reads.fasta
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24 -b reads.bam
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25 -g genome.fa
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26 #if $w and str($w).strip():
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27 -w "${w}"
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28 #end if
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29 > methylation_calls.tsv
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30 ]]></command>
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31 <inputs>
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32 <!-- index inputs -->
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33 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
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34 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/>
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35
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36 <!-- variants consensus inputs -->
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37 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
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38 <param type="data" argument="-g" format="fasta" label="The reference genome"/>
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39
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40 <param argument="-w" type="text" optional="true"
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41 label="find variants in window of region chromsome:start-end" />
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42
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43 </inputs>
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44
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45 <outputs>
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46 <!-- variants consensus outputs -->
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47 <data name="output_methylation_calls" format="tabular" from_work_dir="methylation_calls.tsv" label="called methylation sites" />
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48 </outputs>
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49 <tests>
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50 <test>
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51 <!-- index test -->
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52 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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53 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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54
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55 <!-- variants consensus test -->
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56 <param name="b" value="reads.sorted.bam" />
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57 <param name="g" value="draft.fa" />
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58 <param name="w" value="tig00000001:200000-202000" />
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59
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60 <output name="output_methylation_calls" file="methylation_calls.tsv" />
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64 Usage: nanopolish call-methylation [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
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65 Classify nucleotides as methylated or not.
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66
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67 Quickstart tutorial and manual available at:
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68 http://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html
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69
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70 ]]></help>
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71 <expand macro="citations" />
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72 </tool>