| Next changeset 1:22cd2369354b (2017-08-07) |
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Commit message:
Uploaded |
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added:
fastqc_report.xml |
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| diff -r 000000000000 -r 0a2457551e25 fastqc_report.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastqc_report.xml Mon Aug 07 21:40:26 2017 -0400 |
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| @@ -0,0 +1,53 @@ +<tool id="fastqc_report" name="Fastqc report" version="1.0.0"> + <requirements> + <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement> + <requirement type="package" version="1.20.0">r-getopt</requirement> + <requirement type="package" version="1.2">r-rmarkdown</requirement> + <requirement type="package" version="1.8.4">r-plyr</requirement> + <requirement type="package" version="1.1.0">r-stringr</requirement> + <requirement type="package" version="0.4.0">r-highcharter</requirement> + <requirement type="package" version="0.2">r-dt</requirement> + <requirement type="package" version="1.4.2">r-reshape2</requirement> + <requirement type="package" version="4.5.6">r-plotly</requirement> + <requirement type="package" version="0.2.0.1">r-formattable</requirement> + <requirement type="package" version="0.3.5">r-htmltools</requirement> + <requirement type="package" version="0.11.5">fastqc</requirement> + </requirements> + <description> + Implements FastQC analysis and display results in R Markdown html. + </description> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="Error in" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + <regex match="Fatal error" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + </stdio> + <command> + <![CDATA[ + + Rscript '${__tool_directory__}/fastqc_report_render.R' + -r $reads + -p '${__tool_directory__}/fastqc_report.Rmd' + -o $report + -d $report.files_path + + -e $echo + + ]]> + </command> + <inputs> + <param format="fastq,fastq.gz,fastq.bz2,bam,sam" multiple="true" name="reads" type="data" label="Short reads data from history" /> + <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> + </inputs> + <outputs> + <data format="html" name="report" label="fastqc report" /> + </outputs> +</tool> |