Mercurial > repos > mingchen0919 > test_galaxy_tool_generator
changeset 8:571cc9a41c12 draft
test commit message today
| author | mingchen0919 |
|---|---|
| date | Sun, 17 Dec 2017 01:35:50 -0500 |
| parents | 2ceb4048ea29 |
| children | 74d362c8c0c3 |
| files | fastqc.xml tool1.xml |
| diffstat | 2 files changed, 40 insertions(+), 40 deletions(-) [+] |
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--- a/fastqc.xml Sun Dec 17 01:26:54 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -<tool id="tool_template" name="tool name 2" 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool1.xml Sun Dec 17 01:35:50 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>