diff fastqc_report.xml @ 14:2efa46ce2c4c draft

upgrade fastqc_report

--- a/fastqc_report.xml	Mon Oct 16 21:33:31 2017 -0400
+++ b/fastqc_report.xml	Wed Oct 18 22:06:39 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="fastqc_report" name="Fastqc report" version="1.0.1">
+<tool id="fastqc_report" name="Fastqc report" version="2.0.0">
     <description>
         Implements FastQC analysis and display results in R Markdown html.
     </description>
@@ -6,7 +6,7 @@
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <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="1.3">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="0.5.0">r-highcharter</requirement>
@@ -18,38 +18,35 @@
         <requirement type="package" version="0.11.5">fastqc</requirement>
     </requirements>
     <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." />
+        <!--redirecting stderr to a file. "XXX" is used to match with nothing so that tool running won't be interrupted during testing-->
+        <regex match="XXX"
+               source="stderr"
+               level="warning"
+               description="Check the warnings_and_errors.txt file for more details."/>
     </stdio>
     <command>
         <![CDATA[
 
         Rscript '${__tool_directory__}/fastqc_report_render.R'
+            -e $echo
             -r $reads
-            -p '${__tool_directory__}/fastqc_report.Rmd'
+
 		    -o $report
 		    -d $report.files_path
+		    -s $sink_message
 
-		    -e $echo
-
+		    -p '${__tool_directory__}/fastqc_report.Rmd'
         ]]>
     </command>
     <inputs>
-        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" 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?" />
+        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" 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" />
+        <data format="html" name="report" label="fastqc report"/>
+        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
     </outputs>
     <citations>
         <citation type="bibtex">
@@ -62,7 +59,8 @@
         <citation type="bibtex">
             @article{allaire2016rmarkdown,
             title={rmarkdown: Dynamic Documents for R, 2016},
-            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
+            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
             journal={R package version 0.9},
             volume={6},
             year={2016}
@@ -80,7 +78,8 @@
         <citation type="bibtex">
             @misc{plotly2017,
             title = {plotly: Create Interactive Web Graphics via 'plotly.js'},
-            author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy},
+            author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and
+            Marianne Corvellec and Pedro Despouy},
             year = {2017},
             note = {R package version 4.6.0},
             url = {https://CRAN.R-project.org/package=plotly},