diff mothur/tools/mothur/get.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/get.seqs.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/get.seqs.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -38,6 +38,12 @@
    #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__]
   #end if
   --result=#echo ','.join($results)
+	#if $count.__str__ != "None" and len($count.__str__) > 0:
+		--count=$count
+	#end if
+	#if $fastq.__str__ != "None" and len($fastq.__str__) > 0:
+		--fastq=$fastq
+	#end if
  </command>
  <inputs>
   <param name="accnos" type="data" format="accnos" label="accnos - Accession Names"/>
@@ -49,6 +55,8 @@
   <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/>
   <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
   <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/>
+	<param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+	<param name="fastq" type="data" format="fastq" optional="true" label="count - a count_table" help="fastq - allows you to select sequences from your fastq file"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
@@ -77,7 +85,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="package" version="1.27">mothur</requirement>
+<requirement type = "package" version ="1.33">mothur</requirement>
  </requirements>
  <tests>
  </tests>
@@ -102,5 +110,7 @@
 .. _list.seqs: http://www.mothur.org/wiki/list.seqs
 .. _get.seqs: http://www.mothur.org/wiki/Get.seqs
 
+v.1.27.0 : Updated to Mothur 1.33, added count and fastq params
+
  </help>
 </tool>