Mercurial > repos > iuc > mothur_get_groups
diff get.groups.xml @ 2:1715be05e718 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:15:38 -0400 |
| parents | e2b43f377f7d |
| children |
line wrap: on
line diff
--- a/get.groups.xml Tue Sep 05 16:51:18 2017 -0400 +++ b/get.groups.xml Tue Mar 20 22:15:38 2018 -0400 @@ -7,58 +7,69 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@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 +## 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 '$design_in' design_in.dat && +ln -s '$column_in' column_in.dat && +ln -s '$phylip_in' phylip_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 +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 + #if $column_in: + ,column=column_in.dat + #end if + #if $phylip_in: + ,phylip=phylip_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"/> + <param name="group_in" type="data" format="mothur.groups,mothur.count_table" optional="true" label="group or count_table file"/> + <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/> + <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"/> <conditional name="groupnames"> <param name="source" type="select" label="Select Group Names from"> <option value="groups">A List of Group Names</option> @@ -78,9 +89,12 @@ <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"/> + <param name="phylip_in" type="data" format="mothur.lower.dist,mothur.square.dist" optional="true" label="phylip - Distance Matrix you would like to select distances from" + help="must be a phylip-formatted distance matrix"/> + <param name="column_in" type="data" format="mothur.pair.dist" optional="true" label="column - Distance Matrix you would like to select distances from" + help="must be a column-formatted distance matrix"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -110,6 +124,12 @@ <data name="design_out" format="mothur.design" from_work_dir="design_in*.pick.*" label="${tool.name} on ${on_string}: pick.design"> <filter>design_in</filter> </data> + <data name="phylip_out" format_source="phylip_in" from_work_dir="phylip_in*.pick.*" label="${tool.name} on ${on_string}: pick.phylip"> + <filter>phylip_in</filter> + </data> + <data name="column_out" format="mothur.pair.dist" from_work_dir="column_in*.pick.*" label="${tool.name} on ${on_string}: pick.column"> + <filter>column_in</filter> + </data> </outputs> <tests> <test><!-- test with group file --> @@ -117,6 +137,7 @@ <param name="source" value="groups"/> <param name="groups" value="forest,pasture"/> <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with accnos file --> @@ -124,6 +145,7 @@ <param name="source" value="accnos"/> <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/> <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with accnos file and most extra files--> @@ -143,11 +165,32 @@ <output_collection name="sharedfiles" count="36"> <element name="0.38" md5="3c78742e0a480ca3353f9b591fc9bf36" ftype="mothur.shared"/> </output_collection> + <param name="savelog" value="true"/> + <expand macro="logfile-test"/> + </test> + <test><!-- test with distance matrix --> + <param name="group_in" value="amazon_withgroups.count_table" ftype="mothur.count_table"/> + <param name="source" value="accnos"/> + <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/> + <param name="column_in" value="amazon.pair.dist" ftype="mothur.pair.dist"/> + <param name="phylip_in" value="amazon.dist" ftype="mothur.square.dist"/> + <output name="column_out" ftype="mothur.pair.dist"> + <assert_contents> + <expand macro="test-column-format"/> + <has_text text="U68589"/> + </assert_contents> + </output> + <output name="phylip_out" ftype="mothur.square.dist"> + <assert_contents> + <expand macro="test-dist-format"/> + <has_text text="U68589"/> + </assert_contents> + </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -162,7 +205,6 @@ .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline .. _get.groups: https://www.mothur.org/wiki/Get.groups -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>