Mercurial > repos > iuc > pycoqc

annotate pycoqc.xml @ 2:d65cec95072e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 6bada3b3ee8791dd7fc2689f8a6023313cb4a0c4
author iuc
date Mon, 25 Sep 2023 08:28:59 +0000
parents a6f21ef054b3
children
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3e8602b5ce6f "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"?>
3e8602b5ce6f "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
d65cec95072e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 6bada3b3ee8791dd7fc2689f8a6023313cb4a0c4
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3 <description>
d65cec95072e 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
d65cec95072e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 6bada3b3ee8791dd7fc2689f8a6023313cb4a0c4
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5 </description>
0
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6 <macros>
3e8602b5ce6f "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>
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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9 <expand macro="requirements"/>
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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10
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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11 <expand macro="version_command"/>
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12
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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13 <command detect_errors="exit_code"><![CDATA[
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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14 pycoQC
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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15 --min_pass_qual '$min_pass_qual'
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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16 --min_pass_len '$min_pass_len'
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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17 #if $filter_calibration:
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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18 '$filter_calibration'
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19 #end if
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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20 #if $filter_duplicated:
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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21 '$filter_duplicated'
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22 #end if
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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23 --min_barcode_percent '$min_barcode_percent'
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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24 --report_title '$report_title'
2
d65cec95072e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 6bada3b3ee8791dd7fc2689f8a6023313cb4a0c4
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25 ## can be implemented in future - --template_file
d65cec95072e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 6bada3b3ee8791dd7fc2689f8a6023313cb4a0c4
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26 ## can be implemented in future - --config_file
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27 #if $skip_coverage_plot
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28 '$skip_coverage_plot'
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29 #end if
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30 --sample '$sample'
2
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31 ## can be implemented in future --default_config
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32 --summary_file '$summary_file'
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33 ## can be implemented in future --barcode_file
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34 #if $bam_file:
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35 --bam_file '$bam_file'
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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36 #end if
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37 --html_outfile '$out_html'
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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38 #if $out_json:
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39 --json_outfile '$out_json'
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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40 #end if
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41 ]]></command>
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42 <inputs>
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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43 <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)" />
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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44 <!-- <param argument="barcode_file" type="data" format="txt" label="" /> -->
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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45 <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"/>
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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46 <param name="output_json_bool" type="boolean" checked="true" label="Output JSON Summary File?"/>
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47 <param argument="--min_pass_qual" type="integer" value="7" min="0" label="Minimum quality to consider a read as 'pass'" />
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48 <param argument="--min_pass_len" type="integer" value="0" min="0" label="Minimum read length to consider a read as 'pass'"/>
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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49 <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" />
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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50 <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)" />
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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51 <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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52 <param argument="--report_title" type="text" value="PycoQC report" label="Title to use in the html report" />
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53 <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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54 <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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55 </inputs>
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56 <outputs>
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57 <!-- standard -->
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58 <data name="out_html" format="html" label="${tool.name} on ${on_string}: HTML Report"/>
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59 <data name="out_json" format="json" label="${tool.name} on ${on_string}: JSON Summary">
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60 <filter>output_json_bool</filter>
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61 </data>
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62 </outputs>
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63 <tests>
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64 <!-- #1 default -->
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65 <test expect_num_outputs="2">
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66 <param name="summary_file" value="test.txt"/>
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67 <output name="out_html">
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68 <assert_contents>
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69 <has_line line="&lt;!doctype html&gt;"/>
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70 <has_n_lines n="300"/>
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71 </assert_contents>
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72 </output>
1
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73 <output name="out_json" file="test.json" lines_diff="2"/>
0
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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77 .. class:: infomark
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78
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79 **What it does**
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80
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81 @WID@
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82
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83 **Input**
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84
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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85 - Guppy Sequencing Summary Output (tsv)
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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86 - Aligned Reads (bam) (Optional)
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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87
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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88 **Output**
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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89
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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90 - Output QC Report (HTML)
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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91 - Output QC Metrics (JSON)
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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92
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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93
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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94 **References**
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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95
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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96 @REFERENCES@
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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97 ]]></help>
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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98 <expand macro="citations"/>
3e8602b5ce6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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99 </tool>