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annotate albacore_1D.xml @ 0:f8e25d69167d draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
author jdv
date Wed, 30 Aug 2017 02:47:27 -0400
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f8e25d69167d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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1 <tool id="albacore_1D" name="Albacore 1D" version="1.2.6">
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3 <description>ONT production 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="1.2.6">albacore</requirement>
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10 </requirements>
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11 -->
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13 <!-- ***************************************************************** -->
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15 <version_command>read_fast5_basecaller.py --version | perl -wnE'print "$1\n" for /\(version ([^\)]+)\)/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__/albacore_1D.py $input $output \${GALAXY_SLOTS:-1}
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24 ]]>
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25 </command>
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27 <!-- ***************************************************************** -->
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29 <inputs>
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31 <param name="input" type="data" format="fast5_archive" label="Input reads" />
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33 </inputs>
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35 <!-- ***************************************************************** -->
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37 <outputs>
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39 <data name="output" format="fastq" label="${tool.name} on ${on_string} (called.fastq)" />
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41 </outputs>
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43 <!-- ***************************************************************** -->
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45 <tests>
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46 <test>
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47 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" />
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48 <output name="output" file="test_data.fastq" compare="diff" />
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49 </test>
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50 </tests>
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52 <!-- ***************************************************************** -->
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54 <help>
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55 <![CDATA[
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57 **Description**
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59 Albacore is a tool for basecalling Oxford Nanopore reads. It is distributed by
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60 ONT to authorized community members only and thus is not packaged through
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61 Galaxy or Bioconda. End users are responsible for installing and testing the
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62 albacore software themselves and ensuring that it is in the galaxy user $PATH.
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64 The Galaxy wrapper has modified albacore to take a gzip tarball of FAST5 reads
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65 as input, such as can be produced by `poretools combine`, and always outputs a
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66 single FASTQ file.
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68 This is the 1D basecaller.
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70 ]]>
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71 </help>
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73 <!-- ***************************************************************** -->
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75 <citations>
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76 </citations>
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78 </tool>