Mercurial > repos > jdv > nanopolish

annotate nanopolish_index.xml @ 12:f64b148e6189 draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit ba4c46d7717e3acd346c9c6bf0bbc9bbecccc190
author jdv
date Fri, 09 Mar 2018 21:56:08 -0500
parents 32cb27adeb34
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1 <tool id="nanopolish_index" name="Nanopolish::index" version="0.8.5">
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3 <description>Index FASTQ reads in FAST5 file</description>
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5 <!-- ***************************************************************** -->
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7 <requirements>
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8 <requirement type="package" version="0.8.5">nanopolish</requirement>
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9 </requirements>
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11 <!-- ***************************************************************** -->
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13 <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command>
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15 <!-- ***************************************************************** -->
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17 <command detect_errors="aggressive">
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18 <![CDATA[
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20 perl $__tool_directory__/nanopolish_index.pl
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22 --reads $input_reads
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23 --fast5 $input_fast5
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24 --out $out_index
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26 ]]>
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27 </command>
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29 <!-- ***************************************************************** -->
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31 <inputs>
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33 <param name="input_reads" type="data" format="fasta,fastq" label="Input reads (FASTA/Q)" />
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34 <param name="input_fast5" type="data" format="fast5.tar" label="Input reads (FAST5)" />
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36 </inputs>
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38 <!-- ***************************************************************** -->
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40 <outputs>
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42 <data name="out_index" format="tar" label="${tool.name} on ${on_string}" />
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44 </outputs>
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46 <!-- ***************************************************************** -->
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48 <tests>
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49 <test>
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50 <param name="input_reads" value="called.fa" ftype="fasta" />
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51 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
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52 <output name="out_index" file="index.tar" compare="sim_size" delta="100"/>
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53 </test>
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54 </tests>
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56 <!-- ***************************************************************** -->
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58 <help>
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59 <![CDATA[
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61 **Description**
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63 Nanopolish is a software package for signal-level analysis of Oxford Nanopore
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64 sequencing data. Nanopolish can calculate an improved consensus sequence for a
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65 draft genome assembly, detect base modifications, call SNPs and indels with
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66 respect to a reference genome and more.
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68 The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
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69 as input, such as can be produced by `poretools combine`, and always outputs a
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70 single FASTQ file.
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72 This is the `index` module.
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74 ]]>
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75 </help>
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77 <!-- ***************************************************************** -->
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79 <citations>
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80 </citations>
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82 </tool>