Mercurial > repos > iuc > mothur_tree_shared
diff tree.shared.xml @ 0:ffeb8cd81f04 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:16:26 -0400 |
| parents | |
| children | 506ad7182cfb |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tree.shared.xml Fri May 19 05:16:26 2017 -0400 @@ -0,0 +1,169 @@ +<tool profile="16.07" id="mothur_tree_shared" name="Tree.shared" version="@WRAPPER_VERSION@.0"> + <description>Generate a newick tree for dissimilarity among groups</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 "$input.dist" input_dist.dat && + #if not $input.source == "shared": + ln -s "$input.name" input_name.dat && + #end if + + echo 'tree.shared( + #if $input.source == "shared": + shared=input_dist.dat, + #if $input.groups: + groups=${ str($input.groups).replace(",","-") }, + #end if + #if $input.label: + label=${ str($input.label).replace(",","-") }, + #end if + #if $input.subsampling.use == "yes": + #if $input.subsampling.subsample: + subsample=$input.subsampling.subsample, + #else + subsample=T, + #end if + #if $input.subsampling.iters: + iters="$input.subsampling.iters, + #end if + #end if + #elif $input.source == "column": + column=input_dist.dat, + name=input_name.dat, + #elif $input.source == "phylip": + phylip=input_dist.dat, + #if $input.name: + name=input_name.dat, + #end if + #else + count=input_name.dat, + #end if + #if $calc: + calc=${ str($calc).replace(",","-") }, + #end if + processors='\${GALAXY_SLOTS:-8}' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <conditional name="input"> + <param name="source" type="select" label="Select input format"> + <option value="shared">OTU Shared</option> + <option value="column">Pairwise Column Distance Matrix</option> + <option value="phylip">Phylip Distance Matrix</option> + <option value="count">Count file</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" 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 - Names"/> + </when> + <when value="shared"> + <param name="dist" type="data" format="mothur.shared" label="shared - OTU Shared"/> + <param name="label" type="select" label="label - OTU Labels" multiple="true"> + <options> + <filter type="data_meta" ref="dist" key="labels"/> + </options> + </param> + <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> + <options> + <filter type="data_meta" ref="dist" key="groups"/> + </options> + </param> + <conditional name="subsampling"> + <param name="use" type="select" label="subsample"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)" help="Should not exceed the number of sequences in any group"/> + <param name="iters" type="integer" value="" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="count"> + <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> + <param name="name" type="data" format="mothur.count_table" label="count - count_table file"/> + </when> + </conditional> + <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> + <expand macro="calc-common"/> + <!-- set default option(s) --> + <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> + <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> + </param> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="tre" format="mothur.tre" from_work_dir="input_dist*.tre" label="${tool.name} on ${on_string}: tre"> + <filter>input['source'] != 'shared'</filter> + </data> + <collection name="trefiles" type="list" label="${tool.name} on ${on_string}: tre"> + <filter>input['source'] == 'shared'</filter> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.tre" format="mothur.tre"/> + </collection> + </outputs> + <tests> + <test><!-- test with phylip and defaults --> + <param name="source" value="phylip"/> + <param name="dist" value="env.dist"/> + <output name="tre" md5="c74a88ed448aad2d07059eda0b4161e9" ftype="mothur.tre"/> + <expand macro="logfile-test"/> + </test> + <test><!-- test with shared and subsampling --> + <param name="source" value="shared"/> + <param name="dist" value="amazon.an.shared"/> + <param name="use" value="yes"/> + <param name="calc" value="jclass"/> + <output_collection name="trefiles" count="108"> + <element name="jclass.0.32.all" md5="b8adfa6e41397b3815768f987836d102" ftype="mothur.tre"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with shared and label and group select and all calculators --> + <param name="source" value="shared"/> + <param name="dist" value="amazon.an.shared"/> + <param name="label" value="0.05,0.22,0.32"/> + <param name="groups" value="forest,pasture"/> + <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs,sharedobserved"/> + <output_collection name="trefiles" count="117"> + <element name="canberra.0.32" md5="477b061d738d24a7476dd4c90d9666cf" ftype="mothur.tre"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with column and name file --> + <param name="source" value="column"/> + <param name="dist" value="amazon.pair.dist"/> + <param name="name" value="amazon1.names"/> + <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. For calc parameter choices see: https://www.mothur.org/wiki/Calculators + +.. _tree.shared: https://www.mothur.org/wiki/Tree.shared + +]]> + </help> + <expand macro="citations"/> +</tool>