Mercurial > repos > iuc > mothur_phylo_diversity
diff phylo.diversity.xml @ 0:917aa3b39ccd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:54:48 -0400 |
| parents | |
| children | 292c7c4d2789 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phylo.diversity.xml Fri May 19 05:54:48 2017 -0400 @@ -0,0 +1,134 @@ +<tool profile="16.07" id="mothur_phylo_diversity" name="Phylo.diversity" version="@WRAPPER_VERSION@.0"> + <description>Alpha Diversity calculates unique branch length</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 "$tree" tree.dat && + ln -s "$name" name.dat && + ln -s "$count" count.dat && + #if $grouping.use == "yes": + ln -s "$grouping.group" grouping.group.dat && + #end if + + echo 'phylo.diversity( + tree=tree.dat, + #if $grouping.use == "yes": + group=grouping.group.dat, + #if $grouping.groups: + groups=${ str($grouping.groups).replace(",","-") }, + #end if + #end if + #if $name: + name=name.dat, + #end if + iters=$iters, + freq=$freq, + scale=$scale, + collect=$collect, + rarefy=$rarefy, + summary=$summary, + #if $count: + count=count.dat, + #end if + processors='\${GALAXY_SLOTS:-8}' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/> + <conditional name="grouping"> + <param name="use" type="select" label="Analyze by group using a Group file"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/> + <param name="groups" type="select" multiple="true" label="groups - Groups to display"> + <help>All groups displayed if none are selected.</help> + <options> + <filter type="data_meta" ref="group" key="groups"/> + </options> + </param> + </when> + <when value="no"/> + </conditional> + <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file for the tree"/> + <param name="iters" type="integer" value="1000" min="0" label="iters - Number of iterations to try (default 1000)"/> + <param name="freq" type="float" value="100" min="0.0" label="freq - Reporting frequency" help="if between 0 and 100, the percentage of sequences to sample, if greater than one - report every n iterations"/> + <param name="scale" type="boolean" truevalue="true" falsevalue="false" checked="false" label="scale - Scale output to the number of sequences sampled"/> + <param name="rarefy" type="boolean" truevalue="true" falsevalue="false" checked="false" label="rarefy - Calculate the rarefaction data"/> + <param name="summary" type="boolean" truevalue="true" falsevalue="false" checked="true" label="summary - Generate a summary file"/> + <param name="collect" type="boolean" truevalue="true" falsevalue="false" checked="false" label="collect - Create a collectors curve"/> + <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="summary_out" format="tabular" from_work_dir="tree*.phylodiv.summary" label="${tool.name} on ${on_string}: summary"> + <filter>summary</filter> + </data> + <data name="rarefaction_out" format="tabular" from_work_dir="tree*.phylodiv.rarefaction" label="${tool.name} on ${on_string}: rarefaction"> + <filter>rarefy</filter> + </data> + <data name="collectors_out" format="tabular" from_work_dir="tree*.phylodiv" label="${tool.name} on ${on_string}: collectors"> + <filter>collect</filter> + </data> + </outputs> + <tests> + <test><!-- test with tree file only --> + <param name="tree" value="treetest.tre" ftype="mothur.tre"/> + <param name="use" value="no"/> + <output name="summary_out" md5="a9feb4031094b555baf62e0165dd3637" ftype="tabular"/> + <expand macro="logfile-test"/> + </test> + <test><!-- test with tree file and group file and all outputs --> + <param name="tree" value="treetest.tre" ftype="mothur.tre"/> + <param name="use" value="yes"/> + <param name="group" value="treetest.groups"/> + <param name="groups" value="orange,green"/> + <param name="rarefy" value="true"/> + <param name="collect" value="true"/> + <output name="summary_out" md5="27375ea164ad39fb56b9606023cae504" ftype="tabular"/> + <output name="rarefaction_out" ftype="tabular"> + <assert_contents> + <has_text text="numSampled"/> + <has_text text="orange"/> + <has_text text="green"/> + </assert_contents> + </output> + <output name="collectors_out" ftype="tabular"> + <assert_contents> + <has_text text="numSampled"/> + <has_text text="orange"/> + <has_text text="green"/> + </assert_contents> + </output> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + + +**Command Documentation** + +The phylo.diversity_ command calculates alpha diversity as the total of the unique branch length. + +.. _phylo.diversity: https://www.mothur.org/wiki/Phylo.diversity + +v.1.21.0: Updated to Mothur 1.33, added count parameter + +]]> + </help> + <expand macro="citations"/> +</tool>