| Next changeset 1:3a2f2e24c37e (2021-03-11) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" |
|
added:
macros.xml pycoqc.xml test-data/test.json test-data/test.txt |
| b |
| diff -r 000000000000 -r 6fd0573c0e93 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 02 21:09:07 2021 +0000 |
| [ |
| @@ -0,0 +1,30 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">2.5.2</token> + <token name="@PROFILE@">20.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">pycoqc</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>pycoQC --version</version_command> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex">@online{, + author = {Tommaso Leonardi and Adrien Leger}, + title = {pycoQC}, + year = 2021, + url = {https://github.com/tleonardi/pycoQC}, + urldate = {2021-03-02} + }</citation> + </citations> + </xml> + <token name="@WID@"><![CDATA[ +*pycoqc* computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. + ]]></token> + <token name="@REFERENCES@"><![CDATA[ +More information are available on the `website <https://tleonardi.github.io/pycoQC/>`_. + ]]></token> +</macros> |
| b |
| diff -r 000000000000 -r 6fd0573c0e93 pycoqc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pycoqc.xml Tue Mar 02 21:09:07 2021 +0000 |
| [ |
| @@ -0,0 +1,97 @@ +<?xml version="1.0"?> +<tool id="pycoqc" name="Pycoqc" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + + <expand macro="version_command"/> + + <command detect_errors="exit_code"><![CDATA[ +pycoQC +--min_pass_qual '$min_pass_qual' +--min_pass_len '$min_pass_len' +#if $filter_calibration: + '$filter_calibration' +#end if +#if $filter_duplicated: + '$filter_duplicated' +#end if +--min_barcode_percent '$min_barcode_percent' +--report_title '$report_title' +## TODO in future - --template_file +## TODO in future - --config_file +#if $skip_coverage_plot + '$skip_coverage_plot' +#end if +--sample '$sample' +## TODO in future --default_config +--summary_file '$summary_file' +## TODO in future --barcode_file +#if $bam_file: + --bam_file '$bam_file' +#end if +--html_outfile '$out_html' +#if $out_json: + --json_outfile '$out_json' +#end if + ]]></command> + <inputs> + <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)" /> + <!-- <param argument="barcode_file" type="data" format="txt" label="" /> --> + <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"/> + <param name="output_json_bool" type="boolean" checked="true" label="Output JSON Summary File?"/> + <param argument="--min_pass_qual" type="integer" value="7" min="0" label="Minimum quality to consider a read as 'pass'" /> + <param argument="--min_pass_len" type="integer" value="0" min="0" label="Minimum read length to consider a read as 'pass'"/> + <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" /> + <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)" /> + <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" /> + <param argument="--report_title" type="text" value="PycoQC report" label="Title to use in the html report" /> + <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" /> + <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"/> + </inputs> + <outputs> + <!-- standard --> + <data name="out_html" format="html" label="${tool.name} on ${on_string}: HTML Report"/> + <data name="out_json" format="json" label="${tool.name} on ${on_string}: JSON Summary"> + <filter>output_json_bool</filter> + </data> + </outputs> + <tests> + <!-- #1 default --> + <test expect_num_outputs="2"> + <param name="summary_file" value="test.txt"/> + <output name="out_html"> + <assert_contents> + <has_line line="<!doctype html>"/> + <has_n_lines n="300"/> + </assert_contents> + </output> + <output name="out_json" file="test.json"/> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +@WID@ + +**Input** + +- Guppy Sequencing Summary Output (tsv) +- Aligned Reads (bam) (Optional) + +**Output** + +- Output QC Report (HTML) +- Output QC Metrics (JSON) + + +**References** + +@REFERENCES@ + ]]></help> + <expand macro="citations"/> +</tool> |
| b |
| diff -r 000000000000 -r 6fd0573c0e93 test-data/test.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.json Tue Mar 02 21:09:07 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1260 @@\n+{\n+ "pycoqc": {\n+ "version": "2.5.2",\n+ "date": "02/03/21"\n+ },\n+ "All Reads": {\n+ "run": {\n+ "run_duration": 0.07199815538194444,\n+ "active_channels": 375,\n+ "runid_number": 1,\n+ "barcodes_number": 0\n+ },\n+ "basecall": {\n+ "reads_number": 1000,\n+ "bases_number": 3233722,\n+ "N50": 7421,\n+ "len_percentiles": [\n+ 5.0,\n+ 196.89,\n+ 225.82000000000002,\n+ 239.97,\n+ 257.96000000000004,\n+ 273.0,\n+ 281.94,\n+ 297.86,\n+ 305.0,\n+ 317.82,\n+ 327.9,\n+ 336.0,\n+ 342.88,\n+ 350.87,\n+ 362.86,\n+ 370.84999999999997,\n+ 379.68,\n+ 385.0,\n+ 395.0,\n+ 406.81,\n+ 422.40000000000003,\n+ 435.58,\n+ 447.0,\n+ 459.31000000000006,\n+ 475.0,\n+ 491.5,\n+ 509.74,\n+ 520.6500000000001,\n+ 541.0,\n+ 557.0,\n+ 582.7,\n+ 603.8299999999999,\n+ 625.72,\n+ 661.3600000000001,\n+ 688.6600000000001,\n+ 703.6500000000001,\n+ 727.0,\n+ 759.52,\n+ 789.86,\n+ 843.83,\n+ 870.8000000000001,\n+ 906.1300000000002,\n+ 939.3199999999999,\n+ 974.71,\n+ 1019.56,\n+ 1050.3,\n+ 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| b |
| diff -r 000000000000 -r 6fd0573c0e93 test-data/test.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.txt Tue Mar 02 21:09:07 2021 +0000 |
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