Mercurial > repos > mingchen0919 > rmarkdown_fastqc_report

changeset 0:0a2457551e25 draft

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Uploaded
author mingchen0919
date Mon, 07 Aug 2017 21:40:26 -0400
parents
children 22cd2369354b
files fastqc_report.xml
diffstat 1 files changed, 53 insertions(+), 0 deletions(-) [+]
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--- /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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+<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>