diff bdss_client_sra.xml @ 22:89cc5b026494 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 8d95d985955944734cd00ac94346e1197a4feb20-dirty

--- a/bdss_client_sra.xml	Sat Oct 14 19:54:57 2017 -0400
+++ b/bdss_client_sra.xml	Sat Oct 14 22:59:06 2017 -0400
@@ -24,6 +24,7 @@
             Rscript '${__tool_directory__}/bdss_client_sra_render.R'
                 -i '$sra_ids_se'
                 -p '$sra_ids_pe'
+                -f $format
                 -e $echo
 
                 -r $report
@@ -46,12 +47,12 @@
     <outputs>
         <data format="html" name="report" label="BDSS client report"/>
         <!--list dataset collection for single end SRA data-->
-        <collection type="list" name="list_collection" label="Fastq-dump (single end reads)">
-            <discover_datasets pattern="__name_and_ext__" directory="read_files_directory" />
+        <collection type="list" name="list_collection" label="BDSS download data (single end reads)">
+            <discover_datasets pattern="__name_and_ext__" directory="se_read_files_directory" />
         </collection>
         <!--list:paired dataset collection for paired end SRA data-->
-        <collection type="list:paired" name="list_collection" label="Fastq-dump (paired end reads)">
-            <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="read_files_directory"/>
+        <collection type="list:paired" name="list:paired_collection" label="BDSS download data (paired end reads)">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="pe_read_files_directory" />
         </collection>
         <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
     </outputs>