Mercurial > repos > jdv > nanopolish

annotate nanopolish_extract.xml @ 2:e4b6d4a53f2e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
author jdv
date Tue, 03 Oct 2017 21:23:56 -0400
parents a5db82bec597
children 36cc4ae4160e
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1 <tool id="nanopolish_extract" name="Nanopolish::extract" version="0.7.2">
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3 <description>FAST5 to FASTQ/A extraction</description>
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5 <!-- ***************************************************************** -->
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7 <!--
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8 <requirements>
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9 <requirement type="package" version="0.7.2">nanopolish</requirement>
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10 </requirements>
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11 -->
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13 <!-- ***************************************************************** -->
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15 <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command>
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17 <!-- ***************************************************************** -->
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19 <command detect_errors="aggressive">
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20 <![CDATA[
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22 python3 $__tool_directory__/nanopolish_extract.py $input $output \${GALAXY_SLOTS:-1}
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24 ]]>
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25 </command>
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27 <!-- ***************************************************************** -->
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29 <inputs>
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31 <param name="input" type="data" format="fast5.tar" label="Input reads" />
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32 <param name="out_format" type="select" label="Output format">
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33 <option value="fastq" selected="true">fastq</option>
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34 <option value="fasta">fasta</option>
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35 </param>
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37 </inputs>
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39 <!-- ***************************************************************** -->
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41 <outputs>
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43 <data name="output" format="fastqsanger" label="${tool.name} on ${on_string}">
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44 <change_format>
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45 <when input="out_format" value="fasta" format="fasta" />
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46 </change_format>
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47 </data>
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49 </outputs>
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51 <!-- ***************************************************************** -->
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53 <tests>
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54 <test>
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55 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
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56 <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
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57 </test>
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58 </tests>
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60 <!-- ***************************************************************** -->
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62 <help>
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63 <![CDATA[
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65 **Description**
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67 Nanopolish is a software package for signal-level analysis of Oxford Nanopore
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68 sequencing data. Nanopolish can calculate an improved consensus sequence for a
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69 draft genome assembly, detect base modifications, call SNPs and indels with
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70 respect to a reference genome and more.
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72 The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
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73 as input, such as can be produced by `poretools combine`, and always outputs a
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74 single FASTQ file.
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75
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76 This is the `extract` module.
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78 ]]>
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79 </help>
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81 <!-- ***************************************************************** -->
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83 <citations>
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84 </citations>
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86 </tool>