Mercurial > repos > jdv > scrappie

annotate scrappie_raw.xml @ 3:632c50fe83ba draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
author jdv
date Tue, 03 Oct 2017 21:50:49 -0400
parents b4721d6ecae2
children
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1 <tool id="scrappie_raw" name="Scrappie::raw" version="1.0.0">
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3 <description>ONT development basecaller</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="1.0.0">scrappie</requirement>
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10 </requirements>
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11 -->
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13 <!-- ***************************************************************** -->
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15 <version_command>scrappie version | perl -wnE'print "$1\n" for /scrappie (.+)/g'</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__/scrappie_raw.py $input $output \${GALAXY_SLOTS:-1}
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24 ]]>
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25 </command>
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27 <!-- ***************************************************************** -->
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29 <inputs>
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31 <param name="input" type="data" format="fast5.tar" label="Input reads" />
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33 </inputs>
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35 <!-- ***************************************************************** -->
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37 <outputs>
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39 <data name="output" format="fasta" label="${tool.name} on ${on_string} (called.fasta)" />
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41 </outputs>
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43 <!-- ***************************************************************** -->
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45 <tests>
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46 <!-- multithreaded output is non-deterministic, so simply compare file
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47 sizes -->
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48 <test>
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49 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
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50 <output name="output" file="test_data.fasta" compare="sim_size" delta="0" />
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51 </test>
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52 </tests>
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54 <!-- ***************************************************************** -->
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56 <help>
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57 <![CDATA[
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59 **Description**
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61 Scrappie provides recurrent neural network basecalling for Oxford Nanopore
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62 MinION data. It is a technology demonstrator for the Oxford Nanopore
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63 Research Algorithms group. It is designed for improved calling of
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64 homopolymers over nanonet. Scrappie is provided unsupported by Oxford
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65 Nanopore Technologies.
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67 The Galaxy wrapper has modified scrappie to take a gzip tarball of FAST5 reads
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68 as input, such as can be produced by `poretools combine`, and always outputs a
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69 single FASTA file.
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71 This is the raw basecaller.
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73 ]]>
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74 </help>
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76 <!-- ***************************************************************** -->
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78 <citations>
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79 </citations>
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81 </tool>