Mercurial > repos > jjohnson > mothur_toolsuite
diff mothur/tools/mothur/get.seqs.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
---|---|
date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 5265aa9067e0 |
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--- a/mothur/tools/mothur/get.seqs.xml Tue Jun 07 17:35:35 2011 -0400 +++ b/mothur/tools/mothur/get.seqs.xml Tue Jun 07 17:39:06 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="mothur_get_seqs" name="Get.seqs" version="1.16.0"> +<tool id="mothur_get_seqs" name="Get.seqs" version="1.19.0"> <description>Picks sequences by name</description> <command interpreter="python"> mothur_wrapper.py @@ -47,7 +47,7 @@ <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="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/> </inputs> <outputs> @@ -72,7 +72,7 @@ <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 ${on_string}: pick.taxonomy"> + <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> <filter>taxonomy_in != None</filter> </data> </outputs> @@ -92,8 +92,14 @@ **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. +The get.seqs_ command takes a list of sequence names and either a fasta, name_, group_, list_, align.report_ or taxonomy_ 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. +.. _name: http://www.mothur.org/wiki/Name_file +.. _group: http://www.mothur.org/wiki/Group_file +.. _list: http://www.mothur.org/wiki/List_file +.. _align.report: http://www.mothur.org/wiki/Align.seqs +.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline +.. _list.seqs: http://www.mothur.org/wiki/list.seqs .. _get.seqs: http://www.mothur.org/wiki/Get.seqs