diff mothur/tools/mothur/get.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/get.seqs.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,101 @@
+<tool id="mothur_get_seqs" name="Get.seqs" version="1.15.0">
+ <description>Picks sequences by name</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  #import re, os.path
+  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
+  ## adds .pick before the last extension to the input file (except align.report)
+  --cmd='get.seqs'
+  --outputdir='$logfile.extra_files_path'
+  --accnos=$accnos
+  #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 $qfile_in.__str__ != "None" and len($qfile_in.__str__) > 0:
+   --qfile=$qfile_in
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($qfile_in.__str__)) + ":'" + $qfile_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
+  #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.align.report',$os.path.basename($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 $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0:
+   --taxonomy=$taxonomy_in
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__]
+  #end if
+  --result=#echo ','.join($results)
+ </command>
+ <inputs>
+  <param name="accnos" type="data" format="accnos" label="accnos - Accession Names"/>
+  <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
+  <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
+  <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
+  <param name="group_in" type="data" format="groups" optional="true" label="group - Sequences 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="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy"/>
+  <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <!-- format should be set to match input -->
+  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
+   <filter>fasta_in != None</filter>
+  </data>
+  <!-- format should be set to match input -->
+  <data format="qual" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile">
+   <filter>qfile_in != None</filter>
+  </data>
+  <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.names">
+   <filter>name_in != None</filter>
+  </data>
+  <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups">
+   <filter>group_in != None</filter>
+  </data>
+  <data format="align.report" name="alignreport_out" label="${tool.name} on ${on_string}: pick.align.report">
+   <filter>alignreport_in != None</filter>
+  </data>
+  <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list">
+   <filter>list_in != None</filter>
+  </data>
+  <data format="taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy">
+   <filter>taxonomy_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 get.seqs_ command takes a list of sequence names and either a fasta, name, group, list, or align.report file to generate a new file that contains only the sequences in the list. This command may be used in conjunction with the list.seqs command to help screen a sequence collection.
+
+.. _get.seqs: http://www.mothur.org/wiki/Get.seqs
+
+
+ </help>
+</tool>