diff mothur/tools/mothur/screen.seqs.xml @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

--- a/mothur/tools/mothur/screen.seqs.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/screen.seqs.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,12 +1,12 @@
-<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.16.0">
+<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.19.0">
  <description>Screen sequences</description>
  <command interpreter="python">
   mothur_wrapper.py 
   #import re, os.path
   --cmd='screen.seqs'
   #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
-  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.good.\2',$os.path.basename($input.__str__)) + ":'" + $out_file.__str__]
-  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.bad.accnos',$os.path.basename($input.__str__)) + ":'" + $bad_accnos.__str__]
+  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input.__str__)) + ":'" + $out_file.__str__]
+  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.bad.accnos',$os.path.basename($input.__str__)) + ":'" + $bad_accnos.__str__]
   --outputdir='$logfile.extra_files_path'
   --tmpdir='${logfile.extra_files_path}/input'
   --fasta=$input
@@ -34,17 +34,21 @@
   #if $optimize != None and $optimize.__str__ != "None":
    --optimize=$optimize
   #end if
+  #if $input_qfile != None and $input_qfile.__str__ != "None":
+   --qfile=$input_qfile
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_qfile.__str__)) + ":'" + $output_qfile.__str__]
+  #end if
   #if $input_names != None and $input_names.__str__ != "None":
    --name=$input_names
-   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.good.\2',$os.path.basename($input_names.__str__)) + ":'" + $output_names.__str__]
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_names.__str__)) + ":'" + $output_names.__str__]
   #end if
   #if $input_groups != None and $input_groups.__str__ != "None":
    --group=$input_groups
-   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.good.\2',$os.path.basename($input_groups.__str__)) + ":'" + $output_groups.__str__]
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_groups.__str__)) + ":'" + $output_groups.__str__]
   #end if
   #if $input_alignreport != None and $input_alignreport.__str__ != "None":
    --alignreport=$input_alignreport
-   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.good.\2',$os.path.basename($input_alignreport.__str__)) + ":'" + $output_alignreport.__str__]
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_alignreport.__str__)) + ":'" + $output_alignreport.__str__]
   #end if
   --result=#echo ','.join($results)
   --processors=2
@@ -66,18 +70,18 @@
    <option value="maxambig">maxambig</option>
    <option value="maxhomop">maxhomop</option>
   </param>
-  <param name="input_names" type="data" format="names" optional="true" label="name - Sequece Names to screen"/>
+  <param name="input_qfile" type="data" format="qual" optional="true" label="qfile - Sequence Quality file  to screen"/>
+  <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"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="fasta" name="out_file" label="${tool.name} on ${on_string}: good.${input.datatype.file_ext}" >
-   <change_format>
-    <when input_dataset="input" attribute="ext" value="align" format="align"/>
-   </change_format>
+  <data format_source="input" name="out_file" label="${tool.name} on ${on_string}: good.${input.datatype.file_ext}" />
+  <data format="accnos" name="bad_accnos" label="${tool.name} on ${on_string}: bad.accnos" />
+  <data format_source="input_qfile" name="output_qfile" label="${tool.name} on ${on_string}: qfile" >
+   <filter>input_qfile != None</filter>
   </data>
-  <data format="accnos" name="bad_accnos" label="${tool.name} on ${on_string}: bad.accnos" />
   <data format="names" name="output_names" label="${tool.name} on ${on_string}: names" >
    <filter>input_names != None</filter>
   </data>
@@ -104,8 +108,11 @@
 
 **Command Documenation**
 
-The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a names, group, or align.report file. 
+The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name_, group_, or align.report_ file. 
 
+.. _name: http://www.mothur.org/wiki/Name_file
+.. _group: http://www.mothur.org/wiki/Group_file
+.. _align.report: http://www.mothur.org/wiki/Align.seqs
 .. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs