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comparison pycoqc.xml @ 0:6fd0573c0e93 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
author iuc
date Tue, 02 Mar 2021 21:09:07 +0000
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children 3a2f2e24c37e
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-1:000000000000 0:6fd0573c0e93
1 <?xml version="1.0"?>
2 <tool id="pycoqc" name="Pycoqc" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description></description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8
9 <expand macro="version_command"/>
10
11 <command detect_errors="exit_code"><![CDATA[
12 pycoQC
13 --min_pass_qual '$min_pass_qual'
14 --min_pass_len '$min_pass_len'
15 #if $filter_calibration:
16 '$filter_calibration'
17 #end if
18 #if $filter_duplicated:
19 '$filter_duplicated'
20 #end if
21 --min_barcode_percent '$min_barcode_percent'
22 --report_title '$report_title'
23 ## TODO in future - --template_file
24 ## TODO in future - --config_file
25 #if $skip_coverage_plot
26 '$skip_coverage_plot'
27 #end if
28 --sample '$sample'
29 ## TODO in future --default_config
30 --summary_file '$summary_file'
31 ## TODO in future --barcode_file
32 #if $bam_file:
33 --bam_file '$bam_file'
34 #end if
35 --html_outfile '$out_html'
36 #if $out_json:
37 --json_outfile '$out_json'
38 #end if
39 ]]></command>
40 <inputs>
41 <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)" />
42 <!-- <param argument="barcode_file" type="data" format="txt" label="" /> -->
43 <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"/>
44 <param name="output_json_bool" type="boolean" checked="true" label="Output JSON Summary File?"/>
45 <param argument="--min_pass_qual" type="integer" value="7" min="0" label="Minimum quality to consider a read as 'pass'" />
46 <param argument="--min_pass_len" type="integer" value="0" min="0" label="Minimum read length to consider a read as 'pass'"/>
47 <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" />
48 <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)" />
49 <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" />
50 <param argument="--report_title" type="text" value="PycoQC report" label="Title to use in the html report" />
51 <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" />
52 <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"/>
53 </inputs>
54 <outputs>
55 <!-- standard -->
56 <data name="out_html" format="html" label="${tool.name} on ${on_string}: HTML Report"/>
57 <data name="out_json" format="json" label="${tool.name} on ${on_string}: JSON Summary">
58 <filter>output_json_bool</filter>
59 </data>
60 </outputs>
61 <tests>
62 <!-- #1 default -->
63 <test expect_num_outputs="2">
64 <param name="summary_file" value="test.txt"/>
65 <output name="out_html">
66 <assert_contents>
67 <has_line line="&lt;!doctype html&gt;"/>
68 <has_n_lines n="300"/>
69 </assert_contents>
70 </output>
71 <output name="out_json" file="test.json"/>
72 </test>
73 </tests>
74 <help><![CDATA[
75 .. class:: infomark
76
77 **What it does**
78
79 @WID@
80
81 **Input**
82
83 - Guppy Sequencing Summary Output (tsv)
84 - Aligned Reads (bam) (Optional)
85
86 **Output**
87
88 - Output QC Report (HTML)
89 - Output QC Metrics (JSON)
90
91
92 **References**
93
94 @REFERENCES@
95 ]]></help>
96 <expand macro="citations"/>
97 </tool>