diff mothur/tools/mothur/screen.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/screen.seqs.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/screen.seqs.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.23.0">
+<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.24.0">
  <description>Screen sequences</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -57,6 +57,17 @@
   #end if
   --result=#echo ','.join($results)
   --processors=8
+	#if $count.__str__ != "None" and len($count.__str__) > 0:
+		--count=$count
+	#end if
+  #if $summary != None and $summary.__str__ != "None":
+   --summary=$summary
+  #end if
+	#if $contigsreport != None and $contigsreport.__str__ != "None":
+   --contigsreport=$contigsreport
+  #end if
+
+
  </command>
  <inputs>
   <param name="input_fasta" type="data" format="fasta,align" label="fasta - Fasta to screen"/>
@@ -79,7 +90,10 @@
   <param name="input_names" type="data" format="names" optional="true" label="name - Sequence Names to screen"/>
   <param name="input_groups" type="data" format="groups" optional="true" label="group - Groups to screen"/>
   <param name="input_alignreport" type="data" format="align.report" optional="true" label="alignreport - Align Report to screen"/>
+  <param name="summary" type="data" format="synnary" optional="true" label="summary - allows you to enter the summary file created by summary.seqs to save processing time when screening with parameters in the summary file"/>
+  <param name="contigsreport" type="data" format="contigs.report" optional="true" label="contigsreport - file is created by the make.contigs command. If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches"/>
   <param name="input_taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
+	<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" />
@@ -102,7 +116,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="package" version="1.27">mothur</requirement>
+<requirement type = "package" version ="1.33">mothur</requirement>
  </requirements>
  <tests>
  </tests>