Mercurial > repos > iuc > mothur_remove_groups
diff remove.groups.xml @ 0:e7a69b6134c5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:14:41 -0400 |
parents | |
children | 75433aae83fb |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/remove.groups.xml Fri May 19 05:14:41 2017 -0400 @@ -0,0 +1,150 @@ +<tool profile="16.07" id="mothur_remove_groups" name="Remove.groups" version="@WRAPPER_VERSION@.0"> + <description>Remove groups from groups,fasta,names,list,taxonomy</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 + #if $groupnames.source == "other": + ln -s "$groupnames.group_in" groupnames_group_in.dat && + ln -s "$groupnames.fasta_in" groupnames_fasta_in.dat && + ln -s "$groupnames.name_in" groupnames_name_in.dat && + ln -s "$groupnames.list_in" groupnames_list_in.dat && + ln -s "$groupnames.taxonomy_in" groupnames_taxonomy_in.dat && + #else + ln -s "$groupnames.shared_in" groupnames_shared_in.dat && + #end if + + echo 'remove.groups( + #if $groupnames.source == "other": + #if $group_in.is_of_type("mothur.groups"): + group=groupnames_group_in.dat + #else + count=groupnames_group_in.dat + #end if + #if $groupnames.fasta_in: + ,fasta=groupnames_fasta_in.dat + #end if + #if $groupnames.name_in: + ,name=groupnames_name_in.dat + #end if + #if $groupnames.list_in: + ,list=groupnames_list_in.dat + #end if + #if $groupnames.taxonomy_in: + ,taxonomy=groupnames_taxonomy_in.dat + #end if + #else + shared=groupnames_shared_in.dat + #end if + ,groups=${ str($groupnames.groups).replace(",","-") } + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <conditional name="groupnames"> + <param name="source" type="select" label="Select Input Type"> + <option value="shared">shared file</option> + <option value="other">fasta, name, taxonomy, or list with a group file or count table</option> + </param> + <when value="other"> + <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count table - Groups"/> + <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false"> + <options> + <filter type="data_meta" ref="group_in" key="groups"/> + </options> + </param> + <param name="fasta_in" type="data" format="mothur.align,fasta" optional="true" label="fasta - Fasta Sequences"/> + <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> + <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> + <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> + </when> + <when value="shared"> + <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/> + <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false"> + <options> + <filter type="data_meta" ref="shared_in" key="groups"/> + </options> + </param> + </when> + </conditional> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="fasta_out" format_source="fasta_in" from_work_dir="groupnames_fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta"> + <filter>groupnames['source'] == 'other' and groupnames['fasta_in']</filter> + </data> + <data name="group_out" format="mothur.groups" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"> + <filter>groupnames['source'] == 'other' and groupnames['group_in'].ext == 'mothur.groups'</filter> + </data> + <data name="count_out" format="mothur.count_table" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.count_table"> + <filter>groupnames['source'] == 'other' and groupnames['group_in'].ext == 'mothur.count_table'</filter> + </data> + <data name="name_out" format="mothur.names" from_work_dir="groupnames_name_in*.pick.*" label="${tool.name} on ${on_string}: pick.names"> + <filter>groupnames['source'] == 'other' and groupnames['name_in']</filter> + </data> + <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="groupnames_taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy"> + <filter>groupnames['source'] == 'other' and groupnames['taxonomy_in']</filter> + </data> + <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list"> + <filter>groupnames['source'] == 'other' and groupnames['list_in']</filter> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.pick\.dat" format="mothur.list"/> + </collection> + <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: pick.shared"> + <filter>groupnames['source'] == 'shared'</filter> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.pick\.dat" format="mothur.shared"/> + </collection> + </outputs> + <tests> + <test><!-- test with shared file --> + <param name="source" value="shared"/> + <param name="shared_in" value="amazon.an.shared"/> + <param name="groups" value="pasture"/> + <output_collection name="shared_out" count="36"> + <element name="0.26" md5="c5043237225f0292ce1bfbd2766b96ea" ftype="mothur.shared"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with group file and fasta/names/list/taxonomy files --> + <param name="source" value="other"/> + <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> + <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> + <param name="name_in" value="amazon.names" ftype="mothur.names"/> + <param name="list_in" value="amazon.an.list" ftype="mothur.list"/> + <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/> + <param name="groups" value="pasture"/> + <output name="fasta_out" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/> + <output name="taxonomy_out" md5="8fcaadcb5ad40873e270ad7e2cebe7fa" ftype="mothur.seq.taxonomy"/> + <output name="group_out" md5="6d689ead98f3eb1af41f1a78386d0b50" ftype="mothur.groups"/> + <output name="name_out" md5="55dbcadbb414d95bae8a282a93c10e63" ftype="mothur.names"/> + <output_collection name="list_out" count="36"> + <element name="0.26" md5="71282909924de5f43452f1a5dbf623e8" ftype="mothur.list"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + </tests> + <help><![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The remove.groups_ command removes sequences from a specific group or set of groups from the following file types: 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 +.. _remove.groups: https://www.mothur.org/wiki/Remove.groups + +]]> + </help> + <expand macro="citations"/> +</tool>