Mercurial > repos > iuc > mothur_cluster
diff cluster.xml @ 0:8c1b609f566d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:40:08 -0400 |
| parents | |
| children | 6f2cdccbfa48 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cluster.xml Fri May 19 05:40:08 2017 -0400 @@ -0,0 +1,120 @@ +<tool profile="16.07" id="mothur_cluster" name="Cluster" version="@WRAPPER_VERSION@.0"> + <description>Assign sequences to OTUs (Operational Taxonomic Unit)</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 "$matrix.dist" matrix.dist.dat && + ln -s "$matrix.name" matrix.name.dat && + ln -s "$count" count.dat && + + echo 'cluster( + #if $matrix.format == "phylip": + phylip=matrix.dist.dat, + #else + column=matrix.dist.dat, + #end if + #if $matrix.name: + name=matrix.name.dat, + #end if + #if $count: + count=count.dat, + #end if + hard=$hard, + #if float($cutoff) > 0.0: + cutoff=$cutoff, + #end if + precision=$precision, + sim=$sim, + method=$method + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <conditional name="matrix"> + <param name="format" type="select" label="Select a Distance Matrix Format" help=""> + <option value="column">Pairwise Column 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="name" type="data" format="mothur.names" optional="true" label="name - 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="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> + </when> + </conditional> + <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> + <param name="method" type="select" label="method - Select a Clustering Method" help=""> + <option value="furthest">Furthest neighbor</option> + <option value="nearest">Nearest neighbor</option> + <option value="average" selected="true">Average neighbor</option> + <option value="weighted">Weighted</option> + </param> + <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0.0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/> + <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/> + <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths"> + <option value="10">.1</option> + <option value="100" selected="true">.01</option> + <option value="1000">.001</option> + <option value="10000">.0001</option> + <option value="100000">.00001</option> + <option value="1000000">.000001</option> + </param> + <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="rabund" format="mothur.rabund" from_work_dir="matrix.dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> + <data name="sabund" format="mothur.sabund" from_work_dir="matrix.dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> + <data name="otulist" format="mothur.list" from_work_dir="matrix.dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/> + </outputs> + <tests> + <test><!-- test with phylip input --> + <param name="format" value="phylip"/> + <param name="dist" value="amazon.dist"/> + <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/> + <output name="sabund" file="amazon.an.sabund" ftype="mothur.sabund"/> + <output name="otulist" md5="a6bf2a6ef7950b3ee2aa5bff4a662b6d" ftype="mothur.list"/> + <expand macro="logfile-test"/> + </test> + <test><!-- test with column input --> + <param name="format" value="column"/> + <param name="dist" value="amazon.pair.dist"/> + <param name="name" value="amazon.names"/> + <output name="rabund" md5="ec88216404729d0f4a0463e50e60c9ad" ftype="mothur.rabund"/> + <output name="sabund" md5="f2c714531430b98d8cdfd3497468eec2" ftype="mothur.sabund"/> + <output name="otulist" md5="1769463ed0b6680babe5801bf9c0a85c" ftype="mothur.list"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The cluster_ command assign sequences to OTUs (Operational Taxonomy Unit). The assignment is based on a phylip-formatted_distance_matrix_ or a column-formatted_distance_matrix_ and name_ file. It generates a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file. + +.. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix +.. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix +.. _name: https://www.mothur.org/wiki/Name_file +.. _list: https://www.mothur.org/wiki/List_file +.. _rabund: https://www.mothur.org/wiki/Rabund_file +.. _sabund: https://www.mothur.org/wiki/Sabund_file +.. _cluster: https://www.mothur.org/wiki/Cluster + +]]> + </help> + <expand macro="citations"/> +</tool>