Mercurial > repos > jvolkening > nanopore_qc

annotate nanopore_qc.xml @ 0:e0006d8bf849 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
author jvolkening
date Sat, 02 Mar 2024 03:35:34 +0000
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children 73bc3179799c
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e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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1 <tool id="nanopore_qc" name="NanoporeQC" version="0.003">
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2
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3 <description>Quality report for nanopore data</description>
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4
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5 <requirements>
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6 <requirement type="package" version="3.5.0">r-ggplot2</requirement>
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7 <requirement type="package" version="1.1.4">r-dplyr</requirement>
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8 <requirement type="package" version="1.3.1">r-tidyr</requirement>
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9 <requirement type="package" version="2.1.5">r-readr</requirement>
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10 <requirement type="package" version="2.3.8">r-yaml</requirement>
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11 <requirement type="package" version="1.3.0">r-scales</requirement>
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12 <requirement type="package" version="1.4.3">r-futile.logger</requirement>
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13 <requirement type="package" version="1.14.10">r-data.table</requirement>
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14 <requirement type="package" version="1.7.4">r-optparse</requirement>
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15 <requirement type="package" version="0.88">perl-yaml-libyaml</requirement>
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16 </requirements>
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17
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18 <stdio>
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19 <exit_code range="1:" level="fatal" description="Unknown error" />
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20 <exit_code range=":-1" level="fatal" description="Unknown error" />
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21 </stdio>
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23 <version_command>
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24 <![CDATA[
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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25 echo '0.003'
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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26 ]]>
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27 </version_command>
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29 <command>
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30 <![CDATA[
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31
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32 mkdir -p '${html_file.files_path}'
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33
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34 &&
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35
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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36 Rscript '${__tool_directory__}/nanopore_qc.R'
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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37 -i '$input'
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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38 -o '${html_file.files_path}'
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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39 -q '$q_cutoff'
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40 $discard_failed
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41
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42 &&
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43
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44 perl '${__tool_directory__}/yaml_to_html.pl'
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45
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46 '${html_file.files_path}/summary.yaml'
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47 '${html_file.files_path}'
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48 '$html_file'
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49
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50 ]]>
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51 </command>
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52
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53 <inputs>
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54 <param name="input" type="data" format="tabular" label="Basecall summary file from Albacore"/>
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55 <param name="q_cutoff" type="float" value="10" min="0" label="Quality cutoff for QC calculations" />
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56 <param name="discard_failed" type="boolean" checked="false" truevalue="--discard_failed T" falsevalue="" label="Ignore reads failing quality filter" />
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57 </inputs>
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58 <outputs>
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59 <data format="html" name="html_file" label="NanoporeQC on ${on_string}" />
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60 </outputs>
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61 <tests>
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62 <!-- binary image blobs can differ, which is why we use line matching
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63 instead of file matching -->
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64
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65 <!-- quality cutoff 10 -->
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66 <test>
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67 <param name="input" value="sequencing_summary.txt.small" ftype="tabular" />
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68 <param name="q_cutoff" value="10" />
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69 <output name="html_file">
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70 <assert_contents>
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71 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9990&lt;/td&gt;" />
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72 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;7952&lt;/td&gt;" />
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73 </assert_contents>
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74 </output>
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75 </test>
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76
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77 <!-- quality cutoff 6 -->
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78 <test>
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79 <param name="input" value="sequencing_summary.txt.small" ftype="tabular" />
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80 <param name="q_cutoff" value="6" />
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81 <output name="html_file">
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82 <assert_contents>
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83 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9990&lt;/td&gt;" />
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84 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9254&lt;/td&gt;" />
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85 </assert_contents>
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86 </output>
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87 </test>
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88
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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89 <!-- quality cutoff 6, discard filtered -->
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90 <test>
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91 <param name="input" value="sequencing_summary.txt.small" ftype="tabular" />
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92 <param name="q_cutoff" value="6" />
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93 <param name="discard_failed" value="true" />
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94 <output name="html_file">
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95 <assert_contents>
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96 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9107&lt;/td&gt;" />
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97 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9107&lt;/td&gt;" />
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98 </assert_contents>
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99 </output>
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100 </test>
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101
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102 <!-- Dorado output -->
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103 <test>
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104 <param name="input" value="dorado.txt.small" ftype="tabular" />
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105 <param name="q_cutoff" value="6" />
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106 <output name="html_file">
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107 <assert_contents>
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108 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;31&lt;/td&gt;" />
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109 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;29&lt;/td&gt;" />
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110 </assert_contents>
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111 </output>
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112 </test>
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113
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114 </tests>
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115 <help>
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116 <![CDATA[
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117 `NanoporeQC` produces a QC report for nanopore sequencing data. It utilizes
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118 the summary table produced by Albacore, which saves time by avoiding the
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119 need to re-parse the FAST5 read data. `NanoporeQC` was originally forked
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120 from the `minion_qc` codebase (https://github.com/roblanf/minion_qc).
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121
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122 There are only two tuneable parameters. The 'quality cutoff' sets a
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123 threshold for plotting: two summaries are produced for each table and plot
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124 -- one for all reads (with length >= 0) and one for reads with a quality
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125 value greater than the cutoff. 'Ignore reads failing quality filter'
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126 indicates whether to include or exclude failing reads from the QC plots.
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127 ]]>
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128 </help>
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129 <citations>
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130 <citation type='doi'>10.1093/bioinformatics/bty654</citation>
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131 </citations>
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132 </tool>