rmarkdown_fastqc_site: fastqc_site.xml comparison

comparison fastqc_site.xml @ 11:507eec497730 draft

update fastqc site

author	mingchen0919
date	Tue, 07 Nov 2017 16:52:24 -0500
parents	600c39b11913
children	6faa68239cd7

comparison

equal deleted inserted replaced

-:600c39b11913
+:507eec497730
-<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>
 <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 website.
-</description>
 <stdio>
-<regex match="Execution halted"
+<!--redirecting stderr to a file. "XXX" is used to match with nothing so that tool running won't be interrupted during testing-->
-source="both"
+<regex match="XXX"
-level="fatal"
+source="stderr"
-description="Execution halted." />
+level="warning"
-<regex match="Error in"
+description="Check the warnings_and_errors.txt file for more details."/>
-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_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
+		    -o $report
-		    -d $fastqc_site.files_path
+		    -d $report.files_path
+		    -s $sink_message
 		    ## 3. Rmd templates sitting in the tool directory
-		        ## _site.yml and index.Rmd template files
+		    ## _site.yml and index.Rmd template files
--s '${__tool_directory__}/_site.yml'
+-S '${__tool_directory__}/_site.yml'
--i '${__tool_directory__}/index.Rmd'
+-I '${__tool_directory__}/index.Rmd'
 ## other Rmd body template files
-		        -p  '${__tool_directory__}/01_evaluation_overview.Rmd'
+		    -A '${__tool_directory__}/01_evaluation_overview.Rmd'
-		        -a  '${__tool_directory__}/02_fastqc_original_reports.Rmd'
+		    -B '${__tool_directory__}/02_per_base_sequence_quality.Rmd'
-		        -b  '${__tool_directory__}/1_per_base_quality_scores.Rmd'
+		    -C '${__tool_directory__}/03_per_tile_sequence_quality.Rmd'
-		        -c  '${__tool_directory__}/2_per_base_N_content.Rmd'
+		    -D '${__tool_directory__}/04_per_sequence_quality_score.Rmd'
-		        -f  '${__tool_directory__}/3_per_sequence_quality_scores.Rmd'
+		    -E '${__tool_directory__}/05_per_base_sequence_content.Rmd'
-		        -g  '${__tool_directory__}/4_per_sequence_GC_content.Rmd'
+		    -F '${__tool_directory__}/06_per_sequence_gc_content.Rmd'
-		        -h  '${__tool_directory__}/5_per_base_sequence_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 format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_1" type="data" optional="false"
-<param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+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">
 @misc{bioinformatics2014fastqc,
 title={FastQC},
 }
 </citation>
 <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}
 }
 </citation>
 }
 </citation>
 <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},
 journal={Bioinformatics},
 volume={32},

Mercurial > repos > mingchen0919 > rmarkdown_fastqc_site

comparison fastqc_site.xml @ 11:507eec497730 draft