diff mothur/tools/mothur/trim.seqs.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

--- a/mothur/tools/mothur/trim.seqs.xml	Tue Jun 07 17:32:23 2011 -0400
+++ b/mothur/tools/mothur/trim.seqs.xml	Tue Jun 07 17:35:35 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_trim_seqs" name="Trim.seqs" version="1.15.0">
+<tool id="mothur_trim_seqs" name="Trim.seqs" version="1.16.0">
  <description>Trim sequences - primers, barcodes, quality</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -17,6 +17,12 @@
   #if $maxhomop > 0:
    --maxhomop=$maxhomop 
   #end if
+  #if $keepfirst > 0:
+   --keepfirst=$keepfirst 
+  #end if
+  #if $removelast > 0:
+   --removelast=$removelast 
+  #end if
   #if $oligo.add == "yes":
    --oligos=$oligo.oligos
    #if $oligo.bdiffs > 0:
@@ -48,43 +54,47 @@
   <param name="maxlength" type="integer" value="0" label="maxlength - Maximum Sequence Length (default 0, ignored if &#060; 1)"/>
   <param name="maxambig" type="integer" value="-1" label="maxambig - Maximum ambiguous bases (default -1, ignored if &#060; 0)"/>
   <param name="maxhomop" type="integer" value="0" label="maxhomop - Maximum homopolymers (default 0, ignored if &#060; 1)"/>
+  <param name="keepfirst" type="integer" value="0" label="keepfirst - ignored if &#060; 0)" 
+         help="trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements"/>
+  <param name="removelast" type="integer" value="0" label="removelast - ignored if &#060; 0)" 
+         help="removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements."/>
   <conditional name="oligo">
-   <param name="add" type="select" label="add - Trim with an oligos file" help="">
+   <param name="add" type="select" label="add - trim with an oligos file" help="">
     <option value="no">no</option>
     <option value="yes">yes</option>
    </param>
    <when value="no"/>
    <when value="yes">
-    <param name="oligos" type="data" format="oligos" label="oligos - Oligos - barcodes and primers"/>
-    <param name="bdiffs" type="integer" value="0" label="bdiffs - Number of differences to allow in the barcode (default 0)"/>
-    <param name="pdiffs" type="integer" value="0" label="pdiffs - Number of differences to allow in the primer (default 0)"/>
-    <param name="tdiffs" type="integer" value="0" label="tdiffs - Total number of differences to allow in primer and barcode (ignored if &#060; 1)"/>
+    <param name="oligos" type="data" format="oligos" label="oligos - oligos - barcodes and primers"/>
+    <param name="bdiffs" type="integer" value="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
+    <param name="pdiffs" type="integer" value="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
+    <param name="tdiffs" type="integer" value="0" label="tdiffs - total number of differences to allow in primer and barcode (ignored if &#060; 1)"/>
    </when>
   </conditional>
   <conditional name="qual">
-   <param name="add" type="select" label="add - Trim based on a quality file" help="">
+   <param name="add" type="select" label="add - trim based on a quality file" help="">
     <option value="no">no</option>
     <option value="yes">yes</option>
    </param>
    <when value="no"/>
    <when value="yes">
-    <param name="qfile" type="data" format="qual454" label="qfile - 454 Quality File"/>
-    <param name="qaverage" type="integer" value="0" label="qaverage - Remove sequences that have an average base quality below this value (ignored if &#060; 1)"/>
-    <param name="qthreshold" type="integer" value="0" label="qthreshold - Remove sequences that have any base quality below this value (ignored if &#060; 1)"/>
-    <param name="qtrim" type="boolean" truevalue="--qtrim=true" falsevalue="" checked="false" label="qtrim - Trim sequences below qthreshold and put in trim output, else put in scrap "/>
+    <param name="qfile" type="data" format="qual454" label="qfile - 454 quality file"/>
+    <param name="qaverage" type="integer" value="0" label="qaverage - remove sequences that have an average base quality below this value (ignored if &#060; 1)"/>
+    <param name="qthreshold" type="integer" value="0" label="qthreshold - remove sequences that have any base quality below this value (ignored if &#060; 1)"/>
+    <param name="qtrim" type="boolean" truevalue="--qtrim=true" falsevalue="" checked="false" label="qtrim - trim sequences below qthreshold and put in trim output, else put in scrap "/>
    </when>
   </conditional>
-  <param name="flip" type="boolean" truevalue="--flip=true" falsevalue="" checked="false" label="flip - Reverse Complement the trimmed sequences"/>
+  <param name="flip" type="boolean" truevalue="--flip=true" falsevalue="" checked="false" label="flip - reverse complement the trimmed sequences"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <data format="fasta" name="trim_fasta" label="${tool.name} on ${on_string}: trim.fasta"/>
   <data format="qual" name="trim_qual" label="${tool.name} on ${on_string}: trim.qual">
-   <filter>qfile != None and len(qfile) > 0</filter>
+   <filter>qfile != none and len(qfile) > 0</filter>
   </data>
   <data format="fasta" name="scrap_fasta" label="${tool.name} on ${on_string}: scrap.fasta"/>
   <data format="qual454" name="scrap_qual" label="${tool.name} on ${on_string}: scrap.qual">
-   <filter>qfile != None and len(qfile) > 0</filter>
+   <filter>qfile != none and len(qfile) > 0</filter>
   </data>
   <data format="groups" name="groups_file" label="${tool.name} on ${on_string}: groups"/>
  </outputs>
@@ -94,7 +104,7 @@
  <tests>
  </tests>
  <help>
-**Mothur Overview**
+**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,