Mercurial > repos > iuc > ont_fast5_api_compress_fast5

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api commit e83fdc3a33f17709196a0f5567fbec42f9f31922"
author iuc
date Sat, 23 Oct 2021 20:36:18 +0000
parents d8346bcdcbfa
children
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1 <?xml version="1.0"?>
2
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2 <tool id="ont_fast5_api_compress_fast5" name="@TOOL_NAME@ Compress" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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3 <description>multi read file(s)</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <version_command><![CDATA[compress_fast5 -v]]></version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ## initialize
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11 @INITIALIZE@
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12
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13 ## run
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14 compress_fast5
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15 --recursive
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16 ## required
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17 @INPUTPATH@
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18 @SAVEPATH@
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19 @COMPRESSION@
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20 ## optional
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21 @THREADS@
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22
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23 ## create tarball
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24 @TARBALL@
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25 ]]></command>
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26 <inputs>
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27 <expand macro="input"/>
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28 <expand macro="compression">
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29 <option value="vbz" selected="true">VBZ</option>
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30 </expand>
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31 </inputs>
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32 <outputs>
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33 <expand macro="output"/>
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34 </outputs>
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35 <tests>
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36 <!-- #1 default -->
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37 <test expect_num_outputs="1">
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38 <param name="input_path" value="multi.fast5.tar"/>
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39 <output name="out_results">
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40 <assert_contents>
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41 <has_size value="40960"/>
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42 </assert_contents>
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43 </output>
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44 </test>
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45 <!-- #2 -->
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46 <test expect_num_outputs="1">
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47 <param name="input_path" value="multi.fast5.tar"/>
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48 <param name="compression" value="vbz_legacy_v0"/>
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49 <output name="out_results">
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50 <assert_contents>
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51 <has_size value="40960"/>
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52 </assert_contents>
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53 </output>
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54 </test>
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55 <!-- #3 -->
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56 <test expect_num_outputs="1">
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57 <param name="input_path" value="multi.fast5.tar"/>
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58 <param name="compression" value="gzip"/>
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59 <output name="out_results">
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60 <assert_contents>
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61 <has_size value="40960"/>
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62 </assert_contents>
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63 </output>
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 .. class:: infomark
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68
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69 **What it does**
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70
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71 @WID@
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72
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73 *compress_fast5* copies and converts raw data between vbz and gzip compression formats.
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74
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75 **Input**
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76
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77 Multi read file(s) in FAST5 format that are stored in a flat TAR.
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78
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79 **Output**
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80
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81 Multi read FAST5 file(s) containing compressed reads that are stored in a flat TAR. Further detail of HDF5 data management strategies can be found `here <https://support.hdfgroup.org/HDF5/doc/Advanced/FileSpaceManagement/FileSpaceManagement.pdf>`_.
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82
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83 .. class:: infomark
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84
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85 **References**
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86
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87 @REFERENCES@
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88 ]]></help>
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89 <expand macro="citations"/>
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90 </tool>