Mercurial > repos > mingchen0919 > test_galaxy_tool_generator

changeset 4:1649c9af02cc draft

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planemo upload
author mingchen0919
date Sat, 28 Oct 2017 23:40:32 -0400
parents 0304c01cf24b
children c4b9451503bf
files rmarkdown_fastqc.xml tool1.xml
diffstat 2 files changed, 18 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/rmarkdown_fastqc.xml	Sun Oct 08 22:19:11 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<tool id="rmarkdown_fastqc" name="R Markdown Fastqc" version="1.0.0">
-  <requirements>
-    <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
-    <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
-  </requirements>
-</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool1.xml	Sat Oct 28 23:40:32 2017 -0400
@@ -0,0 +1,18 @@
+<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>