Mercurial > repos > mingchen0919 > rmarkdown_fastqc_report

changeset 4:3073b7bd0807 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_report commit ddb1f6aca7619aea2e660b1729367841b56ba4c9
author mingchen0919
date Tue, 08 Aug 2017 09:36:33 -0400
parents 1ed094d8871c
children 3b275377dd27
files fastqc_report.xml
diffstat 1 files changed, 25 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/fastqc_report.xml	Mon Aug 07 21:48:49 2017 -0400
+++ b/fastqc_report.xml	Tue Aug 08 09:36:33 2017 -0400
@@ -1,4 +1,7 @@
 <tool id="fastqc_report" name="Fastqc report" version="1.0.0">
+    <description>
+        Implements FastQC analysis and display results in R Markdown html.
+    </description>
     <requirements>
         <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
@@ -13,9 +16,6 @@
         <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"
@@ -50,4 +50,26 @@
     <outputs>
         <data format="html" name="report" label="fastqc report" />
     </outputs>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{andrews_s,
+                author = {Andrews, S.},
+                keywords = {bioinformatics, ngs, qc},
+                priority = {2},
+                title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
+                url = {http://www.bioinformatics.babraham.ac.uk/projects/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},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        </citation>
+    </citations>
 </tool>
+
+