Mercurial > repos > iuc > ont_fast5_api_multi_to_single_fast5

annotate macros.xml @ 0:1a37f742e7d7 draft

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"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
author iuc
date Fri, 12 Jun 2020 15:07:40 -0400
parents
children f98c015cebd8
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1a37f742e7d7 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">3.1.3</token>
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4 <token name="@TOOL_NAME@">ont_fast5_api:</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">ont-fast5-api</requirement>
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8 <requirement type="package" version="1.10.5">hdf5</requirement>
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9 </requirements>
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10 </xml>
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11
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12 <!-- command -->
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13 <token name="@BATCHSIZE@"><![CDATA[
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14 --batch_size $batch_size
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15 ]]></token>
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16 <token name="@COMPRESSION@"><![CDATA[
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17 #if $compression != 'none'
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18 --compression '$compression'
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19 #end if
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20 ]]></token>
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21 <token name="@INITIALIZE@"><![CDATA[
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22 mkdir -p './data' &&
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23 tar -xf '$input_path' -C './data' &&
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24 ]]></token>
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25 <token name="@INPUTPATH@"><![CDATA[
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26 --input_path './data'
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27 ]]></token>
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28 <token name="@SAVEPATH@"><![CDATA[
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29 --save_path './results'
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30 ]]></token>
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31 <token name="@TARBALL@"><![CDATA[
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32 && find './results' -type f -name '*.fast5' | tar --transform 's/.*\///g' -cvf './results.fast5.tar' --files-from=/dev/stdin
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33 ]]></token>
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34 <token name="@THREADS@"><![CDATA[
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35 --threads \${GALAXY_SLOTS:-4}
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36 ]]></token>
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37
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38 <!-- input -->
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39 <xml name="input" token_argument="--input_path" token_label="multi">
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40 <param argument="@ARGUMENT@" type="data" format="fast5.tar" label="Select @LABEL@ read input file"/>
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41 </xml>
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42 <xml name="batch_size">
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43 <param argument="--batch_size" type="integer" value="4000" min="1" label="Set batch size" help="Number of single reads to include in each multi read file"/>
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44 </xml>
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45 <xml name="compression">
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46 <param argument="compression" type="select" label="Select output compression type">
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47 <yield/>
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48 <option value="vbz_legacy_v0">VBZ legacy v0</option>
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49 <option value="gzip">GZIP</option>
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50 </param>
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51 </xml>
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52
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53 <!-- output -->
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54 <xml name="output">
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55 <data name="out_results" format="fast5.tar" from_work_dir="results.fast5.tar" label="${tool.name} on ${on_string}: Results"/>
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56 </xml>
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57
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58 <!-- help -->
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59 <token name="@WID@"><![CDATA[
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60 *ont_fast5_api* is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.
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61
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62 - concrete implementation of the FAST5 file schema using the generic h5py library
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63 - plain-english-named methods to interact with and reflect the FAST5 file schema
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64 - tools to convert between multi_read and single_read formats
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65 - tools to compress/decompress raw data in files
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66 ]]></token>
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67 <token name="@REFERENCES@"><![CDATA[
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68 More information are available on `github <https://github.com/nanoporetech/ont_fast5_api>`_.
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69 ]]></token>
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70
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71 <xml name="citations">
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72 <citations>
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73 <citation type="bibtex">
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74 @online{ont_fast5_api,
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75 author = {Oxford Nanopore Technologies },
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76 title = {ont_fast5_api},
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77 year = 2020,
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78 url = {https://github.com/nanoporetech/ont_fast5_api},
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79 urldate = {2020-06-01}
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80 }</citation>
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81 </citations>
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82 </xml>
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83 </macros>