diff filter.xml @ 6:3c50a937d7c1 draft

Uploaded

--- a/filter.xml	Thu Mar 26 16:56:09 2015 -0400
+++ b/filter.xml	Wed Apr 15 19:14:23 2015 -0400
@@ -1,18 +1,18 @@
 <tool id="PHYLO_filter" name="Filter and trim" version="1.2.0">
   <description>sequences</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
   <requirements>
     <requirement type="package">yapp_env</requirement>
   </requirements>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
+  <stdio>
+    <expand macro="basic_errors"/>
+  </stdio>
   <version_command>seqmagick --version</version_command>
   <command interpreter="bash">
     filter-wrapper.sh ${config}
   </command>
-  <stdio>
-    <expand macro="basic_errors"/>
-  </stdio>
   <inputs>
     <!-- TODO: can take either fasta+qual or fastq -->
     <param name="plate_id" type="integer" value="1" label="Plate number"/>
@@ -100,4 +100,8 @@
 .. _quality filter documentation: http://fhcrc.github.io/seqmagick/quality_filter.html
 
   </help>
+  <citations>
+    <expand macro="cite_seqmagick"/>
+    <expand macro="cite_biopython"/>
+  </citations>
 </tool>