diff nullarbor_prepare.xml @ 0:f9c1aaf4f592 draft

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nullarbor_prepare.xml	Fri May 03 07:16:27 2019 -0400
@@ -0,0 +1,20 @@
+<tool id="nullarbor_prepare" name="Nullarbor prepare" version="@VERSION@">
+    <description>Prepare a tab file from a collection of paired-end reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command detect_errors="exit_code"><![CDATA[
+    #for $input in $reads:
+      echo -e '$input.element_identifier''\t''$input[0]''\t''$input[1]' >> 'tab_file';
+    #end for
+    ]]></command>
+
+    <inputs>
+        <param name="reads" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="list:paired" label="Paired collection" help="Collection of reads, requires a mininum of 4 isolates to run (due to Roary)"/>
+     </inputs>
+    <outputs>
+        <data name="tab_file" format="tabular"  label="${tool.name} on ${on_string}: Tab file" from_work_dir="tab_file"/>
+    </outputs>
+    <help><![CDATA[
+        ]]></help>
+</tool>