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annotate nanonet_1D.xml @ 1:57447db0ec78 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit 669955c21a5e770a6777269de6b1d2c375a704e3
author jdv
date Fri, 08 Sep 2017 11:03:35 -0400
parents decd5688d719
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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1 <tool id="nanonet_1D" name="Nanonet 1D" version="2.0.0">
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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3 <description>ONT development basecaller</description>
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5 <!-- ***************************************************************** -->
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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7 <!--
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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8 <requirements>
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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9 <requirement type="package" version="2.0.0">nanonet</requirement>
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10 </requirements>
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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11 -->
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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13 <!-- ***************************************************************** -->
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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15 <version_command>echo "2.0.0"</version_command>
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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17 <!-- ***************************************************************** -->
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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19 <command detect_errors="aggressive">
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20 <![CDATA[
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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22 python3 $__tool_directory__/nanonet_1D.py $input $output \${GALAXY_SLOTS:-1}
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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24 ]]>
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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25 </command>
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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27 <!-- ***************************************************************** -->
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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29 <inputs>
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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31 <param name="input" type="data" format="fast5.tar" label="Input reads" />
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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33 </inputs>
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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35 <!-- ***************************************************************** -->
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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37 <outputs>
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39 <data name="output" format="fastq" label="${tool.name} on ${on_string} (called.fastq)" />
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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41 </outputs>
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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43 <!-- ***************************************************************** -->
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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45 <tests>
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46 <!-- multithreaded output is non-deterministic, so simply compare file
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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47 sizes -->
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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48 <test>
1
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49 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
0
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50 <output name="output" file="test_data.fastq" 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 Nanonet provides recurrent neural network basecalling for Oxford Nanopore
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62 MinION data. It represents the first generation of such a basecaller from
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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63 Oxford Nanopore Technologies, and is provided as a technology demonstrator.
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64 Nanonet is provided unsupported by Oxford Nanopore Technologies, see
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65 LICENSE.md for more information.
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67 For training networks, Nanonet leverages currennt to run recurrent neural
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68 networks. Currennt is generally run with GPUs to aid performance but can be
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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69 run in a CPU only environment. The basecaller does not require currennt, and
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70 is written in pure python with minimal requirements.
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72 The Galaxy wrapper has modified nanonet 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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76 This is the 1D basecaller.
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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>