# HG changeset patch
# User mingchen0919
# Date 1513489813 18000
# Node ID 77acf82a58801ded1243809812a39415ed59363a
# Parent  c4b9451503bffec304710dd69af26b95d47cd438
test commit message!!!

diff -r c4b9451503bf -r 77acf82a5880 deseq2.xml
--- a/deseq2.xml	Sat Oct 28 23:46:10 2017 -0400
+++ b/deseq2.xml	Sun Dec 17 00:50:13 2017 -0500
@@ -7,12 +7,34 @@
     <requirement type="package" version="0.5.0">r-dplyr</requirement>
   </requirements>
   <description>some descriptions about the tool.</description>
-  <command>
+  <stdio>
+    <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
+  </stdio>
+  <command><![CDATA[
                     Rscript '${__tool_directory__}/tool_template_render.R'
                         -e $echo
                         -r $report
                         -d $report.files_path
                         -s $sink_message
                         -t '${__tool_directory__}/tool_template.Rmd
-                    </command>
+                    ]]></command>
+  <inputs>
+    <param type="integer" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
+  </inputs>
+  <outputs>
+    <data name="report" format="html" label="tool name report" hidden="false"/>
+    <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
+  </outputs>
+  <help><![CDATA[some help text]]></help>
+  <citations>
+    <citation><![CDATA[
+                    @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>
diff -r c4b9451503bf -r 77acf82a5880 fastqc.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc.xml	Sun Dec 17 00:50:13 2017 -0500
@@ -0,0 +1,40 @@
+<tool id="tool_template" name="tool name" version="1.0.0">
+  <requirements>
+    <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+    <requirement type="package" version="1.20.0">r-getopt</requirement>
+    <requirement type="package" version="1.3">r-rmarkdown</requirement>
+    <requirement type="package" version="0.3.5">r-htmltools</requirement>
+    <requirement type="package" version="0.5.0">r-dplyr</requirement>
+  </requirements>
+  <description>some descriptions about the tool.</description>
+  <stdio>
+    <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
+  </stdio>
+  <command><![CDATA[
+                    Rscript '${__tool_directory__}/tool_template_render.R'
+                        -e $echo
+                        -r $report
+                        -d $report.files_path
+                        -s $sink_message
+                        -t '${__tool_directory__}/tool_template.Rmd
+                    ]]></command>
+  <inputs>
+    <param type="integer" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
+  </inputs>
+  <outputs>
+    <data name="report" format="html" label="tool name report" hidden="false"/>
+    <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
+  </outputs>
+  <help><![CDATA[some help text]]></help>
+  <citations>
+    <citation><![CDATA[
+                    @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>
diff -r c4b9451503bf -r 77acf82a5880 tool1.xml
--- a/tool1.xml	Sat Oct 28 23:46:10 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-<tool id="tool_template" name="tool name" version="1.0.0">
-  <requirements>
-    <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
-    <requirement type="package" version="1.20.0">r-getopt</requirement>
-    <requirement type="package" version="1.3">r-rmarkdown</requirement>
-    <requirement type="package" version="0.3.5">r-htmltools</requirement>
-    <requirement type="package" version="0.5.0">r-dplyr</requirement>
-  </requirements>
-  <description>some descriptions about the tool.</description>
-  <command>
-                    Rscript '${__tool_directory__}/tool_template_render.R'
-                        -e $echo
-                        -r $report
-                        -d $report.files_path
-                        -s $sink_message
-                        -t '${__tool_directory__}/tool_template.Rmd
-                    </command>
-</tool>