Mercurial > repos > sanbi-uwc > mothur_test
diff tools/mothur/get.groups.xml @ 0:ee4fee239fe7 draft default tip
planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
| author | sanbi-uwc |
|---|---|
| date | Fri, 03 Jun 2016 09:32:47 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mothur/get.groups.xml Fri Jun 03 09:32:47 2016 -0400 @@ -0,0 +1,179 @@ +<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="version_command"/> + <command detect_errors="aggressive"><![CDATA[ + echo 'get.groups( + #if $group_in.is_of_type("mothur.groups"): + group=$group_in + #else + count=$group_in + #end if + #if $groupnames.source == 'groups': + #if $groupnames.groups: + ,groups=${ str($groupnames.groups).replace(",","-") } + #end if + #else + ,accnos=$groupnames.accnos + #end if + #if $fasta_in: + ,fasta=$fasta_in + #end if + #if $name_in: + ,name=$name_in + #end if + #if $list_in: + ,list=$list_in + #end if + #if $shared_in: + ,shared=$shared_in + #end if + #if $taxonomy_in: + ,taxonomy=$taxonomy_in + #end if + #if $design_in: + ,design=$design_in + #end if + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur && + + ## move output files to correct destination + prefix="$group_in" && + mv \${prefix%.dat}*.pick.* "$group_out" && + #if $fasta_in: + prefix2="$fasta_in" && + mv \${prefix2%.dat}*.pick.* "$fasta_out" && + #end if + #if $name_in: + prefix2="$name_in" && + mv \${prefix2%.dat}*.pick.* "$name_out" && + #end if + #if $shared_in: + prefix2="$shared_in" && + mkdir sharedout && + mv \${prefix2%.dat}*.pick.* sharedout/ && + #end if + #if $list_in: + prefix2="$list_in" && + mkdir listout && + mv \${prefix2%.dat}*.pick.* listout/ && + #end if + #if $taxonomy_in: + prefix2="$taxonomy_in" && + mv \${prefix2%.dat}*.pick.* "$taxonomy_out" && + #end if + #if $design_in: + prefix2="$design_in" && + mv \${prefix2%.dat}*.pick.* "$design_out" && + #end if + mv mothur.*.logfile "$logfile" + ]]></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" label="groups - Pick groups to include" multiple="true"> + <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> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/> + <data name="group_out" format="mothur.groups" label="${tool.name} on ${on_string}: pick.groups"/> + <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> + <filter>fasta_in</filter> + </data> + <data name="name_out" format="mothur.names" label="${tool.name} on ${on_string}: pick.name"> + <filter>name_in</filter> + </data> + <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: pick.list"> + <filter>list_in</filter> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.pick\.dat" directory="listout" format="mothur.list"/> + </collection> + <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: pick.shared"> + <filter>shared_in</filter> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.pick\.dat" directory="sharedout" format="mothur.shared"/> + </collection> + <data name="taxonomy_out" format="mothur.seq.taxonomy" label="${tool.name} on ${on_string}: pick.taxonomy"> + <filter>taxonomy_in</filter> + </data> + <data name="design_out" format="mothur.design" label="${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 Documenation** + +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 + +]]> + </help> + <expand macro="citations"/> +</tool>