Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

diff collection_list.xml @ 0:78018b735124 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
author mingchen0919
date Mon, 25 Sep 2017 14:28:52 -0400
parents
children 6be61cb4a1d5
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collection_list.xml	Mon Sep 25 14:28:52 2017 -0400
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+<tool id="rmarkdown_collection_list" name="Collection type: list" version="1.0.0">
+    <description>
+        Create a 'list' dataset collection from a set of files in Galaxy history.
+    </description>
+    <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="1.2">r-rmarkdown</requirement>
+        <requirement type="package" version="0.3.5">r-htmltools</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+            Rscript '${__tool_directory__}/collection_list_render.R'
+                -l $file_list
+                -e $echo
+
+                -r $report
+                -o $list_collection
+                -d $list_collection.files_path
+
+                -t '${__tool_directory__}/collection_list.Rmd'
+        ]]>
+    </command>
+    <inputs>
+        <param type="data" name="file_list" multiple="true" />
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+    </inputs>
+    <outputs>
+        <data format="html" name="report" label="fastqc report" />
+        <collection type="list" name="list_collection">
+            <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="files_directory" />
+        </collection>
+    </outputs>
+</tool>
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