diff mothur/tools/mothur/screen.seqs.xml @ 0:3202a38e44d9

Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/screen.seqs.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,121 @@
+<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.15.0">
+ <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__)) + ":'" + $bad_accnos.__str__]
+  --outputdir='$logfile.extra_files_path'
+  --tmpdir='${logfile.extra_files_path}/input'
+  --fasta=$input
+  #if int($start) >= 0:
+   --start=$start
+  #end if
+  #if int($end) >= 0:
+   --end=$end
+  #end if
+  #if int($minlength) >= 0:
+   --minlength=$minlength
+  #end if
+  #if int($maxlength) >= 0:
+   --maxlength=$maxlength
+  #end if
+  #if int($maxambig) >= 0:
+   --maxambig=$maxambig
+  #end if
+  #if int($maxhomop) >= 0:
+   --maxhomop=$maxhomop
+  #end if
+  #if int($criteria) >= 0:
+   --criteria=$criteria
+  #end if
+  #if $optimize != None and $optimize.__str__ != "None":
+   --optimize=$optimize
+  #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__]
+  #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__]
+  #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__)) + ":'" + $output_alignreport.__str__]
+  #end if
+  --result=#echo ','.join($results)
+ </command>
+ <inputs>
+  <param name="input" type="data" format="fasta,align" label="fasta - Fasta to screen"/>
+  <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/>
+  <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/>
+  <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/>
+  <param name="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/>
+  <param name="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/>
+  <param name="maxhomop" type="integer" value="-1" label="maxhomop - Remove sequences with homopolymers greater than (ignored when negative)"/>
+  <param name="criteria" type="integer" value="-1" label="criteria - Percent of sequences that an optimize value must match to be retained(ignored when negative)"/>
+  <param name="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters">
+   <option value="start">start</option>
+   <option value="end">end</option>
+   <option value="minlength">minlength</option>
+   <option value="maxlength">maxlength</option>
+   <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_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 ${on_string}: good.fasta" >
+   <change_format>
+    <when input_dataset="input" attribute="ext" value="align" format="align"/>
+   </change_format>
+   <!--
+   <actions>
+    <conditional name="input">
+     <when datatype_isinstance="align">
+      <action type="format" default="align"/>
+     </when>
+    </conditional>
+   </actions>
+   -->
+  </data>
+  <data format="accnos" name="bad_accnos" label="${tool.name} on ${on_string}: bad.accnos" />
+  <data format="names" name="output_names" label="${tool.name} on ${on_string}: names" >
+   <filter>input_names != None</filter>
+  </data>
+  <data format="groups" name="output_groups" label="${tool.name} on ${on_string}: groups" >
+   <filter>input_groups != None</filter>
+  </data>
+  <data format="align.report" name="output_alignreport" label="${tool.name} on ${on_string}: align.report" >
+   <filter>input_alignreport != None</filter>
+  </data>
+ </outputs>
+ <requirements>
+  <requirement type="binary">mothur</requirement>
+ </requirements>
+ <tests>
+ </tests>
+ <help>
+**Mothur Overview**
+
+Mothur_, initiated by Dr. Patrick Schloss and his software development team
+in the Department of Microbiology and Immunology at The University of Michigan,
+provides bioinformatics for the microbial ecology community.
+
+.. _Mothur: http://www.mothur.org/wiki/Main_Page
+
+**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. 
+
+.. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs
+
+
+ </help>
+</tool>