Mercurial > repos > jdv > albacore

annotate albacore_1D.xml @ 8:3dfde840119e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
author jdv
date Mon, 18 Jun 2018 12:20:28 -0400
parents 4d72adba794f
children
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1 <tool id="albacore_1D" name="Albacore 1D" version="2.0.2b">
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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="2.0.2">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 $out_format $demux $disable_filt \${GALAXY_SLOTS:-1}
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24 ]]>
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25 </command>
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27 <!-- ***************************************************************** -->
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29 <inputs>
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31 <param name="input" type="data" format="fast5.tar" label="Input reads" />
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32 <param name="out_format" type="select" label="Output format">
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33 <option value="fastq" selected="true">fastq</option>
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34 <option value="fast5">fast5</option>
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35 </param>
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36 <param name="demux" type="boolean" checked="false" label="Demultiplex" />
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37 <param name="disable_filt" type="boolean" checked="false" label="Disable quality filtering" />
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38 <param name="output_table" type="boolean" checked="false" label="Include table in output" />
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40 </inputs>
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42 <!-- ***************************************************************** -->
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44 <outputs>
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45
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46 <data name="output" format="fastq" label="${tool.name} on ${on_string} (reads)">
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47 <filter>demux is False</filter>
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48 <change_format>
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49 <when input="out_format" value="fast5" format="fast5.tar.gz" />
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50 </change_format>
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51 </data>
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52 <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string} (reads)">
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53 <filter>demux is True and out_format == 'fastq'</filter>
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54 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fastqsanger" />
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55 </collection>
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56 <collection type="list" name="output_collection_fast5" label="${tool.name} on ${on_string} (reads)">
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57 <filter>demux is True and out_format == 'fast5'</filter>
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58 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fast5.tar.gz" />
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59 </collection>
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60 <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${tool.name} on ${on_string} (table)">
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61 <filter>output_table is True</filter>
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62 </data>
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64 </outputs>
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66 <!-- ***************************************************************** -->
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68 <tests>
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69 <test>
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70 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
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71 <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
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72 </test>
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73 <test>
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74 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
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75 <param name="disable_filt" value="true" />
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76 <output name="output" file="test_data_nofilt.fastq" compare="sim_size" delta="0"/>
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77 </test>
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78 </tests>
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80 <!-- ***************************************************************** -->
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82 <help>
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83 <![CDATA[
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85 **Description**
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86
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87 Albacore is a tool for basecalling Oxford Nanopore reads. It is distributed by
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88 ONT to authorized community members only and thus is not packaged through
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89 Galaxy or Bioconda. End users are responsible for installing and testing the
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90 albacore software themselves and ensuring that it is in the galaxy user $PATH.
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91
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92 The Galaxy wrapper has modified albacore to take a gzip tarball of FAST5 reads
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93 as input, such as can be produced by `poretools combine`, and always outputs a
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94 single FASTQ file.
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95
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96 This is the 1D basecaller.
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97
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98 ]]>
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99 </help>
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100
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101 <!-- ***************************************************************** -->
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102
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103 <citations>
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104 </citations>
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105
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106 </tool>