diff fastqc_site.xml @ 11:507eec497730 draft

update fastqc site

--- a/fastqc_site.xml	Tue Aug 15 15:50:21 2017 -0400
+++ b/fastqc_site.xml	Tue Nov 07 16:52:24 2017 -0500
@@ -1,9 +1,9 @@
-<tool id="fastqc_site" name="Fastqc Site" version="1.0.0">
+<tool id="fastqc_site" name="Fastqc Site" version="2.0.0">
     <requirements>
         <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>
@@ -14,22 +14,12 @@
         <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 website.
-    </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." />
+        <!--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[
@@ -37,36 +27,65 @@
         Rscript '${__tool_directory__}/fastqc_site_render.R'
 
             ## 1. input data
-            -r $reads
             -e $echo
+            -r $reads_1
+            -n '$reads_1.name'
+            -R $reads_2
+            -N '$reads_2.name'
+            -c $contaminants
+            -l $limits
 
             ## 2. output report and report site directory
-		    -o $fastqc_site
-		    -d $fastqc_site.files_path
+		    -o $report
+		    -d $report.files_path
+		    -s $sink_message
 
 		    ## 3. Rmd templates sitting in the tool directory
 
-		        ## _site.yml and index.Rmd template files
-                -s '${__tool_directory__}/_site.yml'
-                -i '${__tool_directory__}/index.Rmd'
+		    ## _site.yml and index.Rmd template files
+            -S '${__tool_directory__}/_site.yml'
+            -I '${__tool_directory__}/index.Rmd'
 
-                ## other Rmd body template files
-		        -p  '${__tool_directory__}/01_evaluation_overview.Rmd'
-		        -a  '${__tool_directory__}/02_fastqc_original_reports.Rmd'
-		        -b  '${__tool_directory__}/1_per_base_quality_scores.Rmd'
-		        -c  '${__tool_directory__}/2_per_base_N_content.Rmd'
-		        -f  '${__tool_directory__}/3_per_sequence_quality_scores.Rmd'
-		        -g  '${__tool_directory__}/4_per_sequence_GC_content.Rmd'
-		        -h  '${__tool_directory__}/5_per_base_sequence_content.Rmd'
+            ## other Rmd body template files
+		    -A '${__tool_directory__}/01_evaluation_overview.Rmd'
+		    -B '${__tool_directory__}/02_per_base_sequence_quality.Rmd'
+		    -C '${__tool_directory__}/03_per_tile_sequence_quality.Rmd'
+		    -D '${__tool_directory__}/04_per_sequence_quality_score.Rmd'
+		    -E '${__tool_directory__}/05_per_base_sequence_content.Rmd'
+		    -F '${__tool_directory__}/06_per_sequence_gc_content.Rmd'
+		    -G '${__tool_directory__}/07_per_base_n_content.Rmd'
+		    -H '${__tool_directory__}/08_sequence_length_distribution.Rmd'
+		    -J '${__tool_directory__}/09_sequence_duplication_levels.Rmd'
+		    -K '${__tool_directory__}/10_adapter_content.Rmd'
+		    -L '${__tool_directory__}/11_kmer_content.Rmd'
+
 
         ]]>
     </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?" />
+        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_1" type="data" optional="false"
+               label="Short reads before trimming"
+               help="Short reads data from history. This could be reads before trimming."/>
+        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_2" type="data"
+               label="Short reads after trimming"
+               help="Short reads data from history. This could be reads after trimming."/>
+        <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
+               help="Specifies a non-default file which contains the list of adapter sequences which will be explicitly
+                     searched against the library. The file must contain sets of named adapters
+                     in the form name[tab]sequence.  Lines prefixed with a hash will be ignored."/>
+        <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
+               help="Specifies a non-default file which contains a set of criteria
+                    which will be used to determine the warn/error limits for the
+                    various modules.  This file can also be used to selectively
+                    remove some modules from the output all together.  The format
+                    needs to mirror the default limits.txt file found in the
+                    Configuration folder."/>
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
+               label="Display analysis code in report?"/>
     </inputs>
     <outputs>
-        <data format="html" name="fastqc_site" label="fastqc site" />
+        <data format="html" name="report" label="fastqc site"/>
+        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
     </outputs>
     <citations>
         <citation type="bibtex">
@@ -79,7 +98,8 @@
         <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}
@@ -97,31 +117,14 @@
         <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},
             }
         </citation>
         <citation type="bibtex">
-            @misc{highcharter2017,
-            title = {highcharter: A Wrapper for the 'Highcharts' Library},
-            author = {Joshua Kunst},
-            year = {2017},
-            note = {R package version 0.5.0},
-            url = {https://CRAN.R-project.org/package=highcharter},
-            }
-        </citation>
-        <citation type="bibtex">
-            @misc{formattable2016,
-            title = {formattable: Create 'Formattable' Data Structures},
-            author = {Kun Ren and Kenton Russell},
-            year = {2016},
-            note = {R package version 0.2.0.1},
-            url = {https://CRAN.R-project.org/package=formattable},
-            }
-        </citation>
-        <citation>
             @article{ewels2016multiqc,
             title={MultiQC: summarize analysis results for multiple tools and samples in a single report},
             author={Ewels, Philip and Magnusson, M{\aa}ns and Lundin, Sverker and K{\"a}ller, Max},