Mercurial > repos > jjohnson > mothur_toolsuite
diff mothur/tools/mothur/remove.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
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Mon, 27 Jun 2011 10:12:25 -0500 |
parents | 5265aa9067e0 |
children | 370b3fc4e7d3 |
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--- a/mothur/tools/mothur/remove.lineage.xml Mon Jun 27 09:34:14 2011 -0500 +++ b/mothur/tools/mothur/remove.lineage.xml Mon Jun 27 10:12:25 2011 -0500 @@ -1,4 +1,4 @@ -<tool id="mothur_remove_lineage" name="Remove.lineage" version="1.19.0"> +<tool id="mothur_remove_lineage" name="Remove.lineage" version="1.20.0"> <description>Picks by taxon</description> <command interpreter="python"> mothur_wrapper.py @@ -9,7 +9,7 @@ --cmd='remove.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 +35,16 @@ </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" /> </options> </param> - <param name="taxon" type="text" size="120" label="taxon - Select Taxon"/> + --> + <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"/>