diff mothur/tools/mothur/get.lineage.xml @ 7:7bfe1f843858

Support Mothur v1.20 trim.seqs - added name parameter and optional trim.names output phylo.diversity - group optional, put group and groups in conditional - breaks get.lineage remove.lineage - allow multiple taxons dist.shared - added processors consensus.seqs - add cutoff parameter trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs new tools - chimera.uchime deunique.tree count.seqs shared/relabund files - Column headings refactor lib/galaxy/datatypes/metagenomics.py add filters to label and group selects in tool configs mothur_wrapper.py updated with new tools params

--- a/mothur/tools/mothur/get.lineage.xml	Mon Jun 27 09:34:14 2011 -0500
+++ b/mothur/tools/mothur/get.lineage.xml	Mon Jun 27 10:12:25 2011 -0500
@@ -1,4 +1,4 @@
-<tool id="mothur_get_lineage" name="Get.lineage" version="1.19.0">
+<tool id="mothur_get_lineage" name="Get.lineage" version="1.20.0">
  <description>Picks by taxon</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -9,7 +9,7 @@
   --cmd='get.lineage'
   --outputdir='$logfile.extra_files_path'
   --taxonomy=$taxonomy
-  --taxon="'$re.sub('\(\d+\)','',$taxon.value.__str__)'"
+  --taxon="'$re.sub('(\s|,)+',',',$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__]
@@ -35,14 +35,17 @@
  </command>
  <inputs>
   <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/>
-  <param name="taxons" type="select" size="120" label="Browse Taxons from Taxonomy">
+  <!--
+  <param name="taxons" type="select" size="120" multiple="true" 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" />
+    <filter type="sort_by" name="sorted_taxon" column="1" />
    </options>
   </param>
-  <param name="taxon" type="text" size="120" label="taxon - Select Taxon for filtering"/>
+  -->
+  <param name="taxon" type="text" area="True" size="5x120" label="taxon - Select Taxons for filtering" help="Enter 1 or more taxons separated by whitespace or commas"/>
   <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"/>