Mercurial > repos > iuc > ont_fast5_api_fast5_subset

annotate fast5_subset.xml @ 1:3bdd8fa109b1 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 15:08:23 -0400
parents eb1f4aa80c72
children 33a0ff1bb7df
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1 <?xml version="1.0"?>
1
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2 <tool id="ont_fast5_api_fast5_subset" name="@TOOL_NAME@ Subset" version="@TOOL_VERSION@+galaxy1" profile="18.01">
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3 <description>of 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 <!-- no specific version command for subcommand fast5_subset available -->
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9 <version_command><![CDATA[compress_fast5 -v]]></version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ## initialize
1
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12 mkdir -p './data' &&
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13 tar -xf '$input' -C './data' &&
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14
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15 ## run
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16 fast5_subset
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17 ## required
1
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18 --input './data'
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19 @SAVEPATH@
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20 --read_id_list '$read_id_list'
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21 ## optional
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22 @COMPRESSION@
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23 @BATCHSIZE@
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24 @THREADS@
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25
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26 ## create tarball
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27 @TARBALL@
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28 ]]></command>
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29 <inputs>
1
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30 <expand macro="input" argument="--input"/>
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31 <param argument="--read_id_list" type="data" format="tabular" label="Select file with read IDs" help="Either containing 1 read_id per line or a tabular file with a column named read_id."/>
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32 <expand macro="batch_size"/>
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33 <expand macro="compression">
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34 <option value="none" selected="true">None</option>
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35 <option value="vbz">VBZ</option>
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36 </expand>
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37 </inputs>
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38 <outputs>
1
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39 <expand macro="output"/>
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40 </outputs>
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41 <tests>
1
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42 <!-- #1 default -->
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43 <test expect_num_outputs="1">
1
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44 <param name="input" value="multi.fast5.tar"/>
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45 <param name="read_id_list" value="list.txt"/>
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46 <output name="out_results">
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47 <assert_contents>
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48 <has_size value="30720"/>
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49 </assert_contents>
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50 </output>
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51 </test>
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52 <!-- #2 -->
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53 <test expect_num_outputs="1">
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54 <param name="input" value="multi.fast5.tar"/>
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55 <param name="read_id_list" value="list.txt"/>
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56 <param name="batch_size" value="2"/>
1
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57 <param name="compression" value="gzip"/>
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58 <output name="out_results">
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59 <assert_contents>
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60 <has_size value="51200"/>
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61 </assert_contents>
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62 </output>
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63 </test>
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64 <!-- #3 -->
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65 <test expect_num_outputs="1">
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66 <param name="input" value="multi.fast5.tar"/>
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67 <param name="read_id_list" value="list.txt"/>
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68 <param name="compression" value="vbz"/>
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69 <output name="out_results">
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70 <assert_contents>
1
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71 <has_size value="40960"/>
0
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72 </assert_contents>
1
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73 </output>
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74 </test>
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75 <!-- #4 -->
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76 <test expect_num_outputs="1">
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77 <param name="input" value="multi.fast5.tar"/>
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78 <param name="read_id_list" value="list.txt"/>
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79 <param name="compression" value="vbz_legacy_v0"/>
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80 <output name="out_results">
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81 <assert_contents>
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82 <has_size value="40960"/>
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83 </assert_contents>
0
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84 </output>
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85 </test>
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86 </tests>
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87 <help><![CDATA[
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88 .. class:: infomark
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89
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90 **What it does**
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91
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92 @WID@
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93
1
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94 *fast5_subset* extracts reads from multi read FAST5 file(s) based on a list of read IDs.
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95
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96 **Input**
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97
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98 Multi read file(s) in FAST5 format, that are stored in a flat TAR, and a list of read IDs that should be extracted.
0
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99
eb1f4aa80c72 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 84504d6786e9edf00367739210d6bae78cb42cc8"
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100 **Output**
eb1f4aa80c72 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 84504d6786e9edf00367739210d6bae78cb42cc8"
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101
1
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102 Multi read file(s) in FAST5 format containing a subset of the input file(s). The rseults are are stored in a flat TAR.
0
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103
eb1f4aa80c72 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 84504d6786e9edf00367739210d6bae78cb42cc8"
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104 .. class:: infomark
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105
eb1f4aa80c72 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 84504d6786e9edf00367739210d6bae78cb42cc8"
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106 **References**
eb1f4aa80c72 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 84504d6786e9edf00367739210d6bae78cb42cc8"
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107
eb1f4aa80c72 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 84504d6786e9edf00367739210d6bae78cb42cc8"
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108 @REFERENCES@
eb1f4aa80c72 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 84504d6786e9edf00367739210d6bae78cb42cc8"
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109 ]]></help>
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110 <expand macro="citations"/>
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111 </tool>