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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 4850c9f31e2cf1edb05d5c8cd0c8ec8be12329c9
author iuc
date Mon, 11 Mar 2024 15:25:55 +0000
parents dc1500f42073
children
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6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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1 <?xml version="1.0"?>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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2 <tool id="pycoqc" name="Pycoqc" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2
dc1500f42073 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 6bada3b3ee8791dd7fc2689f8a6023313cb4a0c4
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3 <description>
dc1500f42073 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 6bada3b3ee8791dd7fc2689f8a6023313cb4a0c4
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4 quality control for Nanopore sequencing data
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5 </description>
0
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6 <macros>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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7 <import>macros.xml</import>
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8 </macros>
3
fae03f3d4bf7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 4850c9f31e2cf1edb05d5c8cd0c8ec8be12329c9
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9 <expand macro="xrefs"/>
0
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10 <expand macro="requirements"/>
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6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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12 <expand macro="version_command"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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13
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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14 <command detect_errors="exit_code"><![CDATA[
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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15 pycoQC
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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16 --min_pass_qual '$min_pass_qual'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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17 --min_pass_len '$min_pass_len'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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18 #if $filter_calibration:
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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19 '$filter_calibration'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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20 #end if
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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21 #if $filter_duplicated:
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22 '$filter_duplicated'
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23 #end if
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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24 --min_barcode_percent '$min_barcode_percent'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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25 --report_title '$report_title'
2
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26 ## can be implemented in future - --template_file
dc1500f42073 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 6bada3b3ee8791dd7fc2689f8a6023313cb4a0c4
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27 ## can be implemented in future - --config_file
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28 #if $skip_coverage_plot
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29 '$skip_coverage_plot'
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30 #end if
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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31 --sample '$sample'
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32 ## can be implemented in future --default_config
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33 --summary_file '$summary_file'
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34 ## can be implemented in future --barcode_file
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35 #if $bam_file:
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36 --bam_file '$bam_file'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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37 #end if
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38 --html_outfile '$out_html'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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39 #if $out_json:
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40 --json_outfile '$out_json'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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41 #end if
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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42 ]]></command>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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43 <inputs>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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44 <param argument="--summary_file" type="data" format="txt,tabular" label="A sequencing_summary file" help="Must be generated by Albacore 1.0.0 + (read_fast5_basecaller.py) / Guppy 2.1.3+ (guppy_basecaller)" />
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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45 <!-- <param argument="barcode_file" type="data" format="txt" label="" /> -->
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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46 <param argument="--bam_file" type="data" format="bam" label="An alignment file generated by aligning the reads described in the sequencing_summary file" optional="true"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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47 <param name="output_json_bool" type="boolean" checked="true" label="Output JSON Summary File?"/>
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48 <param argument="--min_pass_qual" type="integer" value="7" min="0" label="Minimum quality to consider a read as 'pass'" />
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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49 <param argument="--min_pass_len" type="integer" value="0" min="0" label="Minimum read length to consider a read as 'pass'"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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50 <param argument="--filter_calibration" type="boolean" checked="false" truevalue="--filter_calibration" falsevalue="" label="Filter Calibration?" help="If yes, reads flagged as calibration strand by the basecaller are removed" />
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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51 <param argument="--filter_duplicated" type="boolean" checked="false" truevalue="--filter_duplicated" falsevalue="" label="Filter Duplicated?" help="If yes, duplicated read_ids are removed but the first occurence is kept (Guppy sometimes outputs the same read multiple times)" />
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52 <param argument="--min_barcode_percent" type="float" value="0.1" label="Minimal percent of total reads to retain barcode label" help="If below, the barcode value is set as unclassified" />
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53 <param argument="--report_title" type="text" value="PycoQC report" label="Title to use in the html report" />
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54 <param argument="--skip_coverage_plot" type="boolean" checked="false" truevalue="--skip_coverage_plot" falsevalue="" label="Skip the coverage plot in HTML report?" help="Useful when using a reference file containing many sequences, i.e. transcriptome" />
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55 <param argument="--sample" type="integer" label="Number of reads will be randomly selected instead of the entire dataset for ploting function" help="(deterministic sampling)" value="100000"/>
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56 </inputs>
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57 <outputs>
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58 <!-- standard -->
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59 <data name="out_html" format="html" label="${tool.name} on ${on_string}: HTML Report"/>
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60 <data name="out_json" format="json" label="${tool.name} on ${on_string}: JSON Summary">
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61 <filter>output_json_bool</filter>
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62 </data>
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63 </outputs>
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64 <tests>
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65 <!-- #1 default -->
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66 <test expect_num_outputs="2">
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67 <param name="summary_file" value="test.txt"/>
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68 <output name="out_html">
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69 <assert_contents>
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70 <has_line line="&lt;!doctype html&gt;"/>
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71 <has_n_lines n="300"/>
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72 </assert_contents>
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73 </output>
1
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74 <output name="out_json" file="test.json" lines_diff="2"/>
0
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78 .. class:: infomark
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79
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80 **What it does**
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81
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82 @WID@
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83
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84 **Input**
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85
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86 - Guppy Sequencing Summary Output (tsv)
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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87 - Aligned Reads (bam) (Optional)
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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88
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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89 **Output**
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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90
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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91 - Output QC Report (HTML)
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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92 - Output QC Metrics (JSON)
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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93
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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94
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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95 **References**
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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96
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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97 @REFERENCES@
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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98 ]]></help>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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99 <expand macro="citations"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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100 </tool>