Mercurial > repos > iuc > ont_fast5_api_fast5_subset

annotate fast5_subset.xml @ 2:33a0ff1bb7df draft

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"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 2df36b6d30fd69ea532a4fd42daf4741363074f3"
author iuc
date Sun, 28 Jun 2020 14:50:52 -0400
parents 3bdd8fa109b1
children 0defe443ea04
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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
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12 mkdir -p './data' &&
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13 tar -xf '$input' -C './data' &&
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14
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15 ## run
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16 fast5_subset
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17 --recursive
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18 ## required
1
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19 --input './data'
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20 @SAVEPATH@
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21 --read_id_list '$read_id_list'
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22 ## optional
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23 @COMPRESSION@
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24 @BATCHSIZE@
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25 @THREADS@
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26
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27 ## create tarball
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28 @TARBALL@
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29 ]]></command>
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30 <inputs>
1
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31 <expand macro="input" argument="--input"/>
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32 <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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33 <expand macro="batch_size"/>
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34 <expand macro="compression">
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35 <option value="none" selected="true">None</option>
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36 <option value="vbz">VBZ</option>
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37 </expand>
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38 </inputs>
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39 <outputs>
1
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40 <expand macro="output"/>
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41 </outputs>
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42 <tests>
1
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43 <!-- #1 default -->
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44 <test expect_num_outputs="1">
1
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45 <param name="input" value="multi.fast5.tar"/>
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46 <param name="read_id_list" value="list.txt"/>
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47 <output name="out_results">
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48 <assert_contents>
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49 <has_size value="30720"/>
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50 </assert_contents>
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51 </output>
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52 </test>
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53 <!-- #2 -->
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54 <test expect_num_outputs="1">
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55 <param name="input" value="multi.fast5.tar"/>
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56 <param name="read_id_list" value="list.txt"/>
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57 <param name="batch_size" value="2"/>
1
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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="51200"/>
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62 </assert_contents>
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63 </output>
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64 </test>
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65 <!-- #3 -->
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66 <test expect_num_outputs="1">
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67 <param name="input" value="multi.fast5.tar"/>
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68 <param name="read_id_list" value="list.txt"/>
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69 <param name="compression" value="vbz"/>
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70 <output name="out_results">
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71 <assert_contents>
1
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72 <has_size value="40960"/>
0
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73 </assert_contents>
1
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74 </output>
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75 </test>
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76 <!-- #4 -->
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77 <test expect_num_outputs="1">
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78 <param name="input" value="multi.fast5.tar"/>
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79 <param name="read_id_list" value="list.txt"/>
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80 <param name="compression" value="vbz_legacy_v0"/>
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81 <output name="out_results">
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82 <assert_contents>
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83 <has_size value="40960"/>
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84 </assert_contents>
0
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85 </output>
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86 </test>
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87 </tests>
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88 <help><![CDATA[
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89 .. class:: infomark
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90
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91 **What it does**
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92
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93 @WID@
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94
1
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95 *fast5_subset* extracts reads from multi read FAST5 file(s) based on a list of read IDs.
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96
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97 **Input**
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98
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99 Multi read file(s) in FAST5 format, that are stored in a flat TAR, and a list of read IDs that should be extracted.
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100
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101 **Output**
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102
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103 Multi read file(s) in FAST5 format containing a subset of the input file(s). The rseults are are stored in a flat TAR.
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104
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105 .. class:: infomark
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106
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107 **References**
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108
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109 @REFERENCES@
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110 ]]></help>
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111 <expand macro="citations"/>
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112 </tool>