diff mothur/tools/mothur/remove.lineage.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/remove.lineage.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,95 @@
+<tool id="mothur_remove_lineage" name="Remove.lineage" version="1.15.0">
+ <description>Picks by taxon</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  #import re, os.path
+  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
+  ## adds .pick before the last extension to the input file
+  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy.__str__)) + ":'" + $taxonomy_out.__str__]
+  --cmd='remove.lineage'
+  --outputdir='$logfile.extra_files_path'
+  --taxonomy=$taxonomy
+  --taxon="'$re.sub('\(\d+\)','',$taxon.value.__str__)'"
+  #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0:
+   --fasta=$fasta_in
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__]
+  #end if
+  #if $group_in.__str__ != "None" and len($group_in.__str__) > 0:
+   --group=$group_in
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__]
+  #end if
+  #if $alignreport_in.__str__ != "None" and len($alignreport_in.__str__) > 0:
+   --alignreport=$alignreport_in
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($alignreport_in.__str__)) + ":'" + $alignreport_out.__str__]
+  #end if
+  #if $list_in.__str__ != "None" and len($list_in.__str__) > 0:
+   --list=$list_in
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__]
+  #end if
+  #if $name_in.__str__ != "None" and len($name_in.__str__) > 0:
+   --name=$name_in
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__]
+   $dups
+  #end if
+  --result=#echo ','.join($results)
+ </command>
+ <inputs>
+  <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy"/>
+  <param name="taxons" type="select" size="120" label="Browse Taxons from Taxonomy">
+   <options from_dataset="taxonomy">
+    <column name="name" index="1"/>
+    <column name="value" index="1"/>
+    <filter type="unique_value" name="unique_taxon" column="1" />
+   </options>
+  </param>
+  <param name="taxon" type="text" size="120" label="taxon - Select Taxon"/>
+  <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
+  <param name="group_in" type="data" format="groups" optional="true" label="group - Groups"/>
+  <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/>
+  <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/>
+  <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
+  <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicate names"/>
+ </inputs>
+ <outputs>
+  <!-- fix format -->
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/>
+  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
+   <filter>fasta_in != None</filter>
+  </data>
+  <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.group">
+   <filter>group_in != None</filter>
+  </data>
+  <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list">
+   <filter>list_in != None</filter>
+  </data>
+  <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name">
+   <filter>name_in != None</filter>
+  </data>
+  <data format="align.report" name="alignreport_out" label="${tool.name} on ${on_string}: pick.align.report">
+   <filter>alignreport_in != 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 remove.lineage_ command reads a taxonomy file and a taxon and generates a new file that contains only the sequences in the that are not from that taxon. You may also include either a fasta, name, group, list, or align.report file to this command and mothur will generate new files for each of those containing only the selected sequences.
+
+.. _remove.lineage: http://www.mothur.org/wiki/Remove.lineage
+
+
+ </help>
+</tool>