annotate single_to_multi_fast5.xml @ 0:ceec541f4955 draft

"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
author iuc
date Fri, 12 Jun 2020 15:08:04 -0400
parents
children ea77d69db382
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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1 <?xml version="1.0"?>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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2 <tool id="ont_fast5_api_single_to_multi_fast5" name="@TOOL_NAME@ Single to multi" version="@TOOL_VERSION@+galaxy0" profile="18.01">
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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3 <description>read file(s)</description>
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4 <macros>
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5 <import>macros.xml</import>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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6 </macros>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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7 <expand macro="requirements"/>
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8 <version_command><![CDATA[single_to_multi -v]]></version_command>
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9 <command detect_errors="exit_code"><![CDATA[
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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10 ## initialize
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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11 @INITIALIZE@
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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12
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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13 ## run
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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14 single_to_multi_fast5
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15 ## required
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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16 @INPUTPATH@
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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17 @SAVEPATH@
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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18 ## optional
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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19 @COMPRESSION@
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20 @BATCHSIZE@
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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21 @THREADS@
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22
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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23 ## create tarball
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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24 @TARBALL@
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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25 ]]></command>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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26 <inputs>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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27 <expand macro="input" label="single"/>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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28 <expand macro="batch_size"/>
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29 <expand macro="compression">
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30 <option value="none" selected="true">None</option>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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31 <option value="vbz">VBZ</option>
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32 </expand>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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33 </inputs>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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34 <outputs>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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35 <expand macro="output"/>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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36 </outputs>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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37 <tests>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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38 <!-- #1 default -->
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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39 <test expect_num_outputs="1">
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40 <param name="input_path" value="single.fast5.tar"/>
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41 <output name="out_results">
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42 <assert_contents>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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43 <has_size value="40960"/>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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44 </assert_contents>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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45 </output>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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46 </test>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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47 <!-- #2 -->
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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48 <test expect_num_outputs="1">
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49 <param name="input_path" value="single.fast5.tar"/>
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50 <param name="batch_size" value="3"/>
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51 <param name="compression" value="vbz"/>
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52 <output name="out_results">
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53 <assert_contents>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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54 <has_size value="51200"/>
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55 </assert_contents>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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56 </output>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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57 </test>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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58 <!-- #3 -->
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59 <test expect_num_outputs="1">
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60 <param name="input_path" value="single.fast5.tar"/>
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61 <param name="compression" value="vbz_legacy_v0"/>
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62 <output name="out_results">
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63 <assert_contents>
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64 <has_size value="40960"/>
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65 </assert_contents>
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66 </output>
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67 </test>
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68 <!-- #4 -->
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69 <test expect_num_outputs="1">
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70 <param name="input_path" value="single.fast5.tar"/>
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71 <param name="compression" value="gzip"/>
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72 <output name="out_results">
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73 <assert_contents>
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74 <has_size value="40960"/>
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75 </assert_contents>
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76 </output>
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77 </test>
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78 </tests>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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79 <help><![CDATA[
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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80 .. class:: infomark
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81
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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82 **What it does**
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83
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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84 @WID@
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85
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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86 *single_to_multi_fast5* converts single read FAST5 files into multi read FAST5 file(s).
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87
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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88 **Input**
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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89
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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90 Single read files in FAST5 format that are stored in a flat TAR.
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91
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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92 **Output**
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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93
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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94 Multi read file(s) in FAST5 format that are stored in a flat TAR.
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95
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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96 .. class:: infomark
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97
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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98 **References**
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99
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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100 @REFERENCES@
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101 ]]></help>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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102 <expand macro="citations"/>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
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103 </tool>