Mercurial > repos > iuc > mothur_dist_shared
diff dist.shared.xml @ 0:7773b7afb53d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:20:24 -0400 |
| parents | |
| children | b7da1494afa1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dist.shared.xml Fri May 19 05:20:24 2017 -0400 @@ -0,0 +1,132 @@ +<tool profile="16.07" id="mothur_dist_shared" name="Dist.shared" version="@WRAPPER_VERSION@.0"> + <description>Generate a phylip-formatted dissimilarity distance matrix among multiple 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 "$otu" otu.dat && + + echo 'dist.shared( + shared=otu.dat, + #if $label: + label=${ str($label).replace(",","-") }, + #end if + #if $groups: + groups=${ str($groups).replace(",","-") }, + #end if + #if $calc: + calc=${ str($calc).replace(",","-") }, + #end if + #if $subsampling.use == "yes": + #if $subsampling.subsample: + subsample=$subsampling.subsample, + #end if + iters=$subsampling.iters, + #end if + output=$output, + processors='\${GALAXY_SLOTS:-8}' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> + <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true"> + <expand macro="labeloptions"/> + </param> + <param name="groups" type="select" label="groups - Groups to analyze" multiple="true"> + <options> + <filter type="data_meta" ref="otu" key="groups"/> + </options> + </param> + <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> + <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="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/> + </when> + <when value="no"/> + </conditional> + <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair"> + <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option> + <option value="square">Phylip formatted Square Matrix</option> + </param> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist files"> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.dist" format="mothur.dist"/> + </collection> + </outputs> + <tests> + <test><!-- test with defaults --> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <output_collection name="distfiles" count="72"> + <element name="thetayc.0.33.lt" md5="c707e43f14c2022f4027e6a2495cbae8" ftype="mothur.dist"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with label,group select and all calculators --> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="label" value="0.05,0.22"/> + <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,structeuclidean,structpearson,sharednseqs,sharedobserved"/> + <output_collection name="distfiles" count="74"> + <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with subsampling --> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="use" value="yes"/> + <param name="subsample" value="10"/> + <param name="iters" value="42"/> + <param name="label" value="0.03,0.33"/> + <param name="calc" value="canberra"/> + <param name="output" value="square"/> + <output_collection name="distfiles" count="6"> + <element name="canberra.0.33.square.std" ftype="mothur.dist"> + <assert_contents> + <has_text text="forest"/> + <has_text text="pasture"/> + </assert_contents> + </element> + </output_collection> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The dist.shared_ command will generate a phylip-formatted_distance_matrix_ that describes the dissimilarity (1-similarity) among multiple groups from a shared_ file. For calc parameter choices see: https://www.mothur.org/wiki/Calculators + +.. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix +.. _shared: https://www.mothur.org/wiki/Shared_file +.. _dist.shared: https://www.mothur.org/wiki/Dist.shared + +v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available. + +]]> + </help> + <expand macro="citations"/> +</tool>