Mercurial > repos > jvolkening > nanopore_qc

annotate nanopore_qc.xml @ 2:5c7848b91964 draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit efc73adf2038b9c6504c60f35202e91dbc7f4d48-dirty
author jvolkening
date Sat, 02 Mar 2024 05:33:33 +0000
parents 73bc3179799c
children
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1 <tool id="nanopore_qc" name="NanoporeQC" version="0.003">
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3 <description>Quality report for nanopore data</description>
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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="1.2.7">r-ragg</requirement>
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16 <requirement type="package" version="0.88">perl-yaml-libyaml</requirement>
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17 </requirements>
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19 <stdio>
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20 <exit_code range="1:" level="fatal" description="Unknown error" />
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21 <exit_code range=":-1" level="fatal" description="Unknown error" />
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22 </stdio>
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24 <version_command>
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25 <![CDATA[
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26 echo '0.003'
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27 ]]>
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28 </version_command>
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30 <command>
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31 <![CDATA[
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33 mkdir -p '${html_file.files_path}'
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35 &&
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37 Rscript '${__tool_directory__}/nanopore_qc.R'
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38 -i '$input'
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39 -o '${html_file.files_path}'
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40 -q '$q_cutoff'
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41 $discard_failed
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43 &&
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45 perl '${__tool_directory__}/yaml_to_html.pl'
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46
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47 '${html_file.files_path}/summary.yaml'
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48 '${html_file.files_path}'
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49 '$html_file'
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50
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51 ]]>
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52 </command>
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53
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54 <inputs>
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55 <param name="input" type="data" format="tabular" label="Basecall summary file from Albacore"/>
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56 <param name="q_cutoff" type="float" value="10" min="0" label="Quality cutoff for QC calculations" />
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57 <param name="discard_failed" type="boolean" checked="false" truevalue="--discard_failed T" falsevalue="" label="Ignore reads failing quality filter" />
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58 </inputs>
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59 <outputs>
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60 <data format="html" name="html_file" label="NanoporeQC on ${on_string}" />
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61 </outputs>
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62 <tests>
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63 <!-- binary image blobs can differ, which is why we use line matching
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64 instead of file matching -->
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65
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66 <!-- quality cutoff 10 -->
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67 <test>
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68 <param name="input" value="sequencing_summary.txt.small" ftype="tabular" />
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69 <param name="q_cutoff" value="10" />
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70 <output name="html_file">
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71 <assert_contents>
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72 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9990&lt;/td&gt;" />
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73 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;7952&lt;/td&gt;" />
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74 </assert_contents>
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75 </output>
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76 </test>
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77
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78 <!-- quality cutoff 6 -->
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79 <test>
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80 <param name="input" value="sequencing_summary.txt.small" ftype="tabular" />
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81 <param name="q_cutoff" value="6" />
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82 <output name="html_file">
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83 <assert_contents>
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84 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9990&lt;/td&gt;" />
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85 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9254&lt;/td&gt;" />
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86 </assert_contents>
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87 </output>
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88 </test>
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89
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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90 <!-- quality cutoff 6, discard filtered -->
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91 <test>
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92 <param name="input" value="sequencing_summary.txt.small" ftype="tabular" />
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93 <param name="q_cutoff" value="6" />
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94 <param name="discard_failed" value="true" />
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95 <output name="html_file">
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96 <assert_contents>
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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 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9107&lt;/td&gt;" />
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99 </assert_contents>
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100 </output>
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101 </test>
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102
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103 <!-- Dorado output -->
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104 <test>
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105 <param name="input" value="dorado.txt.small" ftype="tabular" />
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106 <param name="q_cutoff" value="6" />
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107 <output name="html_file">
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108 <assert_contents>
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109 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;31&lt;/td&gt;" />
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110 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;29&lt;/td&gt;" />
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111 </assert_contents>
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112 </output>
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113 </test>
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114
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115 </tests>
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116 <help>
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117 <![CDATA[
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118 `NanoporeQC` produces a QC report for nanopore sequencing data. It utilizes
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119 the summary table produced by Albacore, which saves time by avoiding the
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120 need to re-parse the FAST5 read data. `NanoporeQC` was originally forked
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121 from the `minion_qc` codebase (https://github.com/roblanf/minion_qc).
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122
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123 There are only two tuneable parameters. The 'quality cutoff' sets a
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124 threshold for plotting: two summaries are produced for each table and plot
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125 -- one for all reads (with length >= 0) and one for reads with a quality
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126 value greater than the cutoff. 'Ignore reads failing quality filter'
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127 indicates whether to include or exclude failing reads from the QC plots.
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128 ]]>
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129 </help>
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130 <citations>
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131 <citation type='doi'>10.1093/bioinformatics/bty654</citation>
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132 </citations>
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133 </tool>