Mercurial > repos > jdv > nanopore_qc
view nanopore_qc.xml @ 0:192df6f6a41e draft
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty
author | jdv |
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date | Mon, 04 Dec 2017 13:02:56 -0500 |
parents | |
children | 8462098b719a |
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<tool id="nanopore_qc" name="NanoporeQC" version="0.001"> <description>QC report for nanopore data</description> <requirements> <requirement type="package" version="2.2.1">r-ggplot2</requirement> <requirement type="package" version="1.8.4">r-plyr</requirement> <requirement type="package" version="1.4.2">r-reshape2</requirement> <requirement type="package" version="0.2.2">r-readr</requirement> <requirement type="package" version="2.1.14">r-yaml</requirement> <requirement type="package" version="0.4.1">r-scales</requirement> <requirement type="package" version="1.4.1">r-futile.logger</requirement> <requirement type="package" version="1.10.4">r-data.table</requirement> <requirement type="package" version="1.3.2">r-optparse</requirement> <requirement type="package" version="1.8">r-mgcv</requirement> <requirement type="package" version="0.66">perl-yaml-libyaml</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Unknown error" /> <exit_code range=":-1" level="fatal" description="Unknown error" /> </stdio> <version_command> <![CDATA[ echo '0.001' ]]> </version_command> <command> <![CDATA[ mkdir -p '${html_file.files_path}' && Rscript '${__tool_directory__}/nanopore_qc.R' -i '$input' -o '${html_file.files_path}' -q '$q_cutoff' && perl '${__tool_directory__}/yaml_to_html.pl' '${html_file.files_path}/summary.yaml' '$html_file' ]]> </command> <inputs> <param name="input" type="data" format="tabular" label="Basecall summary file from Albacore"/> <param name="q_cutoff" type="float" value="10" min="0" label="Quality cutoff for QC calculations" /> </inputs> <outputs> <data format="html" name="html_file" label="NanoporeQC on ${on_string}" /> </outputs> <tests> </tests> <help> <![CDATA[ ]]> </help> <citations> </citations> </tool>