Mercurial > repos > iuc > mothur_get_oturep
diff get.oturep.xml @ 0:e6758f2f744b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:19:22 -0400 |
| parents | |
| children | 07d536eabf6c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get.oturep.xml Fri May 19 05:19:22 2017 -0400 @@ -0,0 +1,256 @@ +<tool profile="16.07" id="mothur_get_oturep" name="Get.oturep" version="@WRAPPER_VERSION@.0"> + <description>Generate a fasta with a representative sequence for each OTU</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 "$otu" otu.dat && + #if $method_condition.method_switch == "distance": + ln -s "$method_condition.matrix_condition.dist" dist.dat && + ln -s "$method_condition.matrix_condition.nameOrCount" nameOrCount.dat && + ln -s "$method_condition.fasta" fasta.dat && + #if $method_condition.pick.type == "yes": + ln -s "$method_condition.pick.group" group.dat && + #end if + #elif $method_condition.method_switch == "abundance": + ln -s "$method_condition.nameOrCount" nameOrCount.dat && + #end if + + echo 'get.oturep( + list=otu.dat, + #if $sorted: + sorted=$sorted, + #end if + #if $label: + label=${ str($label).replace(",","-") }, + #end if + #if $method_condition.method_switch == "distance": + method=distance, + #if $method_condition.matrix_condition.matrix_format == "column": + column=dist.dat, + #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"): + name=nameOrCount.dat, + #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"): + count=nameOrCount.dat, + #end if + #elif $method_condition.matrix_condition.matrix_format == "phylip": + phylip=dist.dat, + #if $method_condition.matrix_condition.nameOrCount: + #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"): + name=nameOrCount.dat, + #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"): + count=nameOrCount.dat, + #end if + #end if + #end if + #if $method_condition.fasta: + fasta=fasta.dat, + #end if + #if $method_condition.pick.type == "yes": + #if $method_condition.pick.group: + group=group.dat, + #end if + #if $method_condition.pick.groups: + groups=${ str($method_condition.pick.groups).replace(",","-") }, + #end if + #end if + large=$method_condition.large + #elif $method_condition.method_switch == "abundance": + method=abundance, + #if $method_condition.nameOrCount.is_of_type("mothur.names"): + name=nameOrCount.dat + #elif $method_condition.nameOrCount.is_of_type("mothur.count_table"): + count=nameOrCount.dat + #end if + #end if + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> + <conditional name="method_condition"> + <param name="method_switch" type="select" label="Method to use for the selection of the representative sequences" help="The distance method finds the sequence with the smallest maximum distance to other sequences. The abundance method chooses the most abundant sequence in the OTU as the representative."> + <option value="distance" selected="true">distance</option> + <option value="abundance">abundance</option> + </param> + <when value="distance"> + <conditional name="matrix_condition"> + <param name="matrix_format" type="select" label="Select a Distance Matrix Format" help=""> + <option value="column">Pairwise Column Distance Matrix</option> + <option value="phylip">Phylip Distance Matrix</option> + </param> + <when value="column"> + <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> + <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/> + </when> + <when value="phylip"> + <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> + <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Name reference"/> + </when> + </conditional> + <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Fasta"/> + <conditional name="pick"> + <param name="type" type="select" label="Parse a group file into abundant and rare groups?" help=""> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="group" type="data" format="mothur.groups" label="group - Group file for the OTU List"/> + <param name="groups" type="select" multiple="true" label="groups - Group Selection (all used if none are selected)"> + <options> + <filter type="data_meta" ref="group" key="groups"/> + </options> + </param> + </when> + </conditional> + <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Distance Matrix is very Large" help="Set this parameter to Yes if your distance matric might not fit in RAM"/> + </when> + <when value="abundance"> + <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/> + </when> + </conditional> + <param name="label" type="select" multiple="true" label="label - OTU Labels"> + <expand macro="labeloptions"/> + </param> + <param name="sorted" type="select" label="sorted - Sort Sequences by"> + <option value="">Don't sort</option> + <option value="name">Sequence Name</option> + <option value="number">Bin Number</option> + <option value="size">Bin Size</option> + <option value="group">Group</option> + </param> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <collection name="names_out" type="list" label="${tool.name} on ${on_string}: rep.names"> + <filter>method_condition['nameOrCount'].ext == "mothur.names"</filter> + <filter>method_condition['matrix_condition']['nameOrCount'].ext == "mothur.names"</filter> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.rep\.names" format="mothur.names"/> + </collection> + <collection name="fasta_out" type="list" label="${tool.name} on ${on_string}: rep.fasta"> + <filter>method_condition['method_switch'] == "distance"</filter> + <filter>method_condition['fasta']</filter> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.rep\.fasta" format="fasta"/> + </collection> + <collection name="count_out" type="list" label="${tool.name} on ${on_string}: rep.count_table"> + <filter>method_condition['nameOrCount'].ext == "mothur.count_table"</filter> + <filter>method_condition['matrix_condition']['nameOrCount'].ext == "mothur.count_table"</filter> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.rep\.count_table" format="mothur.count_table"/> + </collection> + </outputs> + <tests> + <!-- test with distance / phylip --> + <test> + <param name="otu" value="amazon.an.list" ftype="mothur.list"/> + <param name="method_switch" value="distance"/> + <param name="matrix_format" value="phylip"/> + <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/> + <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/> + <output_collection name="names_out" count="36"> + <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <!-- test with distance / column / label select --> + <test> + <param name="otu" value="amazon.an.list" ftype="mothur.list"/> + <param name="method_switch" value="distance"/> + <param name="matrix_format" value="column"/> + <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/> + <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/> + <param name="label" value="unique,0.05,0.27,0.45"/> + <output_collection name="names_out" count="4"> + <element name="0.27" md5="be6dccdd3d4619c3ac465246c826209a" ftype="mothur.names"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <!-- test with distance / fasta / sorting --> + <test> + <param name="otu" value="amazon.an.list" ftype="mothur.list"/> + <param name="method_switch" value="distance"/> + <param name="matrix_format" value="phylip"/> + <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/> + <param name="fasta" value="amazon.fasta" ftype="fasta"/> + <param name="label" value="0.05,0.27"/> + <param name="sorted" value="name"/> + <output_collection name="names_out" count="2"> + <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/> + </output_collection> + <output_collection name="fasta_out" count="2"> + <element name="0.27" md5="a9d9622b6f5fcbe8acdc05df5484ffc4" ftype="fasta"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <!-- test with distance / group file --> + <test> + <param name="otu" value="amazon.an.list" ftype="mothur.list"/> + <param name="method_switch" value="distance"/> + <param name="matrix_format" value="column"/> + <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/> + <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/> + <param name="label" value="unique,0.05,0.27,0.45"/> + <param name="type" value="yes"/> + <param name="group" value="amazon.groups" ftype="mothur.groups"/> + <param name="groups" value="forest,pasture"/> + <output_collection name="names_out" count="8"> + <element name="0.27.pasture" md5="34f87d93fd9ebbefed9754f627f502fd" ftype="mothur.names"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <!-- test with distance / count table --> + <test> + <param name="otu" value="amazon.an.list" ftype="mothur.list"/> + <param name="method_switch" value="distance"/> + <param name="matrix_format" value="phylip"/> + <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/> + <param name="label" value="unique,0.05,0.27"/> + <param name="nameOrCount" value="amazon1.count_table" ftype="mothur.count_table"/> + <output_collection name="count_out" count="3"> + <element name="0.27" md5="6b1afd712825af4bf8cb4ab8304df903" ftype="mothur.count_table"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <!-- test with abundance / count / label --> + <!-- It seems that the content of the result file can vary from one execution to another with the same parameters --> + <test> + <param name="otu" value="amazon.an.list" ftype="mothur.list"/> + <param name="method_switch" value="abundance"/> + <param name="nameOrCount" value="amazon1.count_table" ftype="mothur.count_table"/> + <param name="label" value="0.27,unique"/> + <param name="sorted" value="name"/> + <output_collection name="count_out" count="2"> + <element name="0.27" ftype="mothur.count_table"> + <assert_contents> + <has_text_matching expression="U68\w+\t36" /> + </assert_contents> + </element> + </output_collection> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + + +**Command Documentation** + +The get.oturep_ command generates a fasta-formatted sequence file containing only a representative sequence for each OTU. The opposite of the bin.seqs command. + +.. _get.oturep: https://www.mothur.org/wiki/Get.oturep + +v1.23.0: Updated to Mothur 1.33, added count and method parameter +]]> + </help> + <expand macro="citations"/> +</tool>