diff mothur/tools/mothur/sort.seqs.xml @ 35:95d75b35e4d2

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

--- a/mothur/tools/mothur/sort.seqs.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/sort.seqs.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_sort_seqs" name="Sort.seqs" version="1.24.0">
+<tool id="mothur_sort_seqs" name="Sort.seqs" version="1.25.0">
  <description>put sequences in different files in the same order</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -36,6 +36,9 @@
   #end if
   $large
   --result=#echo ','.join($results)
+#if $count.__str__ != "None" and len($count.__str__) > 0:
+	--count=$count
+#end if
  </command>
  <inputs>
   <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences"/>
@@ -46,6 +49,7 @@
   <param name="taxonomy_in" type="select" format="seq.taxonomy" optional="true" label="taxonomy - taxonomy reference"/>
   <param name="accnos" type="data" format="accnos" optional="true" label="accnos - sort "/>
   <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Datasets are large and may not fit in RAM"/>
+<param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
@@ -69,7 +73,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="package" version="1.27">mothur</requirement>
+<requirement type = "package" version ="1.33">mothur</requirement>
  </requirements>
  <tests>
  </tests>