Mercurial > repos > iuc > mothur_get_groups
diff get.groups.xml @ 1:1e6a7d59a872 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 18:13:49 -0400 |
| parents | 33c6376bd824 |
| children | 378f8103cf1b |
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--- a/get.groups.xml Fri Jun 24 16:31:53 2016 -0400 +++ b/get.groups.xml Thu May 18 18:13:49 2017 -0400 @@ -4,8 +4,11 @@ <import>macros.xml</import> </macros> <expand macro="requirements"/> + <expand macro="stdio"/> <expand macro="version_command"/> - <command detect_errors="aggressive"><![CDATA[ + <command><![CDATA[ + @SHELL_OPTIONS@ + ## create symlinks to input datasets ln -s "$group_in" group_in.dat && ln -s "$fasta_in" fasta_in.dat && @@ -52,6 +55,7 @@ )' | sed 's/ //g' ## mothur trips over whitespace | mothur + | tee mothur.out.log ]]></command> <inputs> <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count_table file"/> @@ -80,7 +84,12 @@ </inputs> <outputs> <expand macro="logfile-output"/> - <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"/> + <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"> + <filter>group_in.ext == "mothur.groups"</filter> + </data> + <data name="count_out" format="mothur.count_table" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.count_table"> + <filter>group_in.ext == "mothur.count_table"</filter> + </data> <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta"> <filter>fasta_in</filter> </data> @@ -143,15 +152,15 @@ @MOTHUR_OVERVIEW@ -**Command Documenation** +**Command Documentation** The get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, fasta, name_, group_, list_, taxonomy_. -.. _name: http://www.mothur.org/wiki/Name_file -.. _group: http://www.mothur.org/wiki/Group_file -.. _list: http://www.mothur.org/wiki/List_file -.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline -.. _get.groups: http://www.mothur.org/wiki/Get.groups +.. _name: https://www.mothur.org/wiki/Name_file +.. _group: https://www.mothur.org/wiki/Group_file +.. _list: https://www.mothur.org/wiki/List_file +.. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline +.. _get.groups: https://www.mothur.org/wiki/Get.groups ]]> </help>