diff mothur/tools/mothur/align.check.xml @ 35:95d75b35e4d2

Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)

--- a/mothur/tools/mothur/align.check.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/align.check.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_align_check" name="Align.check" version="1.19.0">
+<tool id="mothur_align_check" name="Align.check" version="1.20.0">
  <description>Calculate the number of potentially misaligned bases</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -6,7 +6,14 @@
    --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align\.check$:'$out_file
    --outputdir='$logfile.extra_files_path'
    --fasta=$fasta
-   --map=$ss.map
+	 --map=$ss.map
+	 #if $count.__str__ != "None" and len($count.__str__) >0:
+	 	--count=$count
+	 #end if
+	 #if $count.__str__ != "None" and len($count.__str__) >0:
+	 	--name=$name
+	 #end if
+
  </command>
   <inputs>
    <param name="fasta" type="data" format="align" label="fasta - Aligned Sequences"/>
@@ -17,23 +24,23 @@
     </param>
     <when value="cached">
      <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions">
-      <options from_file="mothur_map.loc">
-       <column name="name" index="0" />
-       <column name="value" index="1" />
+      <options from_data_table="mothur_map">
       </options>
      </param>
     </when>
     <when value="history">
      <param name="map" format="map" type="data" label="Secondary Structure Map" />
     </when>
-   </conditional>
+	</conditional>
+   <param name="count" type="data" format="count_table" label="count_table file" optional="true" help="You can also provide a name file associated with your fasta file"/>
+   <param name="name" type="data" format="names" label="names file" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence"/>
   </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <data format="align.check" name="out_file" label="${tool.name} on ${on_string}: align.check"/>
  </outputs>
  <requirements>
-  <requirement type="package" version="1.27">mothur</requirement>
+  <requirement type="package" version="1.33">mothur</requirement>
  </requirements>
  <tests>
  </tests>