Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

diff collection_list.xml @ 1:6be61cb4a1d5 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
author mingchen0919
date Mon, 25 Sep 2017 16:19:52 -0400
parents 78018b735124
children 63e9500cdeec
line wrap: on
line diff
--- a/collection_list.xml	Mon Sep 25 14:28:52 2017 -0400
+++ b/collection_list.xml	Mon Sep 25 16:19:52 2017 -0400
@@ -7,16 +7,17 @@
         <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>
+        <requirement type="package" version="0.5.0">r-dplyr</requirement>
     </requirements>
     <command>
         <![CDATA[
             Rscript '${__tool_directory__}/collection_list_render.R'
                 -l $file_list
                 -e $echo
+                -f $format
 
                 -r $report
-                -o $list_collection
-                -d $list_collection.files_path
+                -d $report.files_path
 
                 -t '${__tool_directory__}/collection_list.Rmd'
         ]]>
@@ -24,11 +25,12 @@
     <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?" />
+        <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/>
     </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" />
+            <discover_datasets pattern="__name_and_ext__" directory="files_directory" />
         </collection>
     </outputs>
 </tool>
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