Mercurial > repos > iuc > mothur_get_groups
view get.groups.xml @ 1:1ce4fb8667ea draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author | iuc |
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date | Tue, 05 Sep 2017 16:51:18 -0400 |
parents | e2b43f377f7d |
children | 1715be05e718 |
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<tool profile="16.07" id="mothur_get_groups" name="Get.groups" version="@WRAPPER_VERSION@.0"> <description>Select groups</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @SHELL_OPTIONS@ ## create symlinks to input datasets ln -s "$group_in" group_in.dat && ln -s "$fasta_in" fasta_in.dat && ln -s "$name_in" name_in.dat && ln -s "$list_in" list_in.dat && ln -s "$shared_in" shared_in.dat && ln -s "$taxonomy_in" taxonomy_in.dat && ln -s "$design_in" design_in.dat && #if $groupnames.source == 'accnos': ln -s "$groupnames.accnos" groupnames.accnos.dat && #end if echo 'get.groups( #if $group_in.is_of_type("mothur.groups"): group=group_in.dat #else count=group_in.dat #end if #if $groupnames.source == 'groups': #if $groupnames.groups: ,groups=${ str($groupnames.groups).replace(",","-") } #end if #else ,accnos=groupnames.accnos.dat #end if #if $fasta_in: ,fasta=fasta_in.dat #end if #if $name_in: ,name=name_in.dat #end if #if $list_in: ,list=list_in.dat #end if #if $shared_in: ,shared=shared_in.dat #end if #if $taxonomy_in: ,taxonomy=taxonomy_in.dat #end if #if $design_in: ,design=design_in.dat #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count_table file"/> <conditional name="groupnames"> <param name="source" type="select" label="Select Group Names from"> <option value="groups">A List of Group Names</option> <option value="accnos">A History Group Name Accnos Dataset</option> </param> <when value="groups"> <param name="groups" type="select" multiple="true" label="groups - Pick groups to include"> <options> <filter type="data_meta" ref="group_in" key="groups"/> </options> </param> </when> <when value="accnos"> <param name="accnos" type="data" format="mothur.accnos" label="accnos - Group Names from your history"/> </when> </conditional> <param name="fasta_in" type="data" format="fasta,mothur.align" optional="true" label="fasta - Fasta Sequences"/> <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/> <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"> <filter>group_in.ext == "mothur.groups"</filter> </data> <data name="count_out" format="mothur.count_table" from_work_dir="group_in*.pick.*" label="${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 ${on_string}: pick.fasta"> <filter>fasta_in</filter> </data> <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.name"> <filter>name_in</filter> </data> <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: pick.list"> <filter>list_in</filter> <discover_datasets pattern="list_in.*?\.(?P<designation>.*)\.pick\.dat" format="mothur.list"/> </collection> <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: pick.shared"> <filter>shared_in</filter> <discover_datasets pattern="shared_in.*?\.(?P<designation>.*)\.pick\.dat" format="mothur.shared"/> </collection> <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy"> <filter>taxonomy_in</filter> </data> <data name="design_out" format="mothur.design" from_work_dir="design_in*.pick.*" label="${tool.name} on ${on_string}: pick.design"> <filter>design_in</filter> </data> </outputs> <tests> <test><!-- test with group file --> <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> <param name="source" value="groups"/> <param name="groups" value="forest,pasture"/> <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> <expand macro="logfile-test"/> </test> <test><!-- test with accnos file --> <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> <param name="source" value="accnos"/> <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/> <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> <expand macro="logfile-test"/> </test> <test><!-- test with accnos file and most extra files--> <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> <param name="source" value="accnos"/> <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/> <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> <param name="name_in" value="amazon1.names" ftype="mothur.names"/> <param name="list_in" value="amazon.an.list" ftype="mothur.list"/> <param name="shared_in" value="amazon.an.shared" ftype="mothur.shared"/> <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> <output name="name_out" md5="1f0324a017e1b71e6ed0af257b0013f3" ftype="mothur.names"/> <output_collection name="listfiles" count="36"> <element name="0.38" md5="49878dfbe53d5144f3bd885c629de822" ftype="mothur.list"/> </output_collection> <output_collection name="sharedfiles" count="36"> <element name="0.38" md5="3c78742e0a480ca3353f9b591fc9bf36" ftype="mothur.shared"/> </output_collection> <expand macro="logfile-test"/> </test> </tests> <help> <![CDATA[ @MOTHUR_OVERVIEW@ **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: 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> <expand macro="citations"/> </tool>