Mercurial > repos > bgruening > nanopolish_methylation

comparison nanopolish_methylation.xml @ 4:a8d4be409446 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 25c22b467760e4784e199125292927bd2274a189-dirty
author bgruening
date Sun, 23 Jun 2019 05:54:36 -0400
parents 02e3c674d917
children 12efe2f03697
comparison
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3:02e3c674d917 4:a8d4be409446
1 <tool id="nanopolish_methylation" name="Nanopolish methylation" version="0.1.0"> 1 <tool id="nanopolish_methylation" name="Nanopolish methylation" version="0.11.1">
2 <description>- Classify nucleotides as methylated or not.</description> 2 <description>- Classify nucleotides as methylated or not.</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
53 > methylation_calls.tsv 53 > methylation_calls.tsv
54 ]]></command> 54 ]]></command>
55 <inputs> 55 <inputs>
56 <!-- index inputs --> 56 <!-- index inputs -->
57 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> 57 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
58 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/> 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"/>
59 59
60 <!-- variants consensus inputs --> 60 <!-- variants consensus inputs -->
61 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> 61 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
62 <conditional name="reference_source"> 62 <conditional name="reference_source">
63 <param name="reference_source_selector" type="select" label="Load reference genome from"> 63 <param name="reference_source_selector" type="select" label="Load reference genome from">
103 <output name="output_methylation_calls" file="methylation_calls.tsv" /> 103 <output name="output_methylation_calls" file="methylation_calls.tsv" />
104 </test> 104 </test>
105 <test> 105 <test>
106 <param name="input_merged" ftype="fasta" value="reads.fasta" /> 106 <param name="input_merged" ftype="fasta" value="reads.fasta" />
107 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> 107 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
108 <param name="reference_source_selector" value="cached" /> 108 <param name="reference_source_selector" value="history" />
109 <param name="ref_file" value="draft"/> 109 <param name="ref_file" value="draft.fa"/>
110 <param name="b" value="reads.sorted.bam" /> 110 <param name="b" value="reads.sorted.bam" />
111 <param name="w" value="tig00000001:200000-202000" /> 111 <param name="w" value="tig00000001:200000-202000" />
112 <param name="batchsize" value="512" /> 112 <param name="batchsize" value="512" />
113 <output name="output_methylation_calls" file="methylation_calls.tsv" /> 113 <output name="output_methylation_calls" file="methylation_calls.tsv" />
114 </test> 114 </test>