Mercurial > repos > iuc > mothur_heatmap_sim
diff heatmap.sim.xml @ 0:002aec843953 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:21:12 -0400 |
parents | |
children | 6c7e2e05f606 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/heatmap.sim.xml Fri May 19 05:21:12 2017 -0400 @@ -0,0 +1,153 @@ +<tool profile="16.07" id="mothur_heatmap_sim" name="Heatmap.sim" version="@WRAPPER_VERSION@.0"> + <description>Generate a heatmap for pariwise similarity</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 "$count" count.dat && + #if $input.source == 'shared': + ln -s "$input.otu" input_otu.dat && + #else + ln -s "$input.dist" input_dist.dat && + #if $input.source == 'column': + ln -s "$input.name" input_name.dat && + #end if + #end if + + echo 'heatmap.sim( + #if $input.source == "shared": + shared=input_otu.dat, + #if $input.label: + label=${ str($input.label).replace(",","-") }, + #end if + #if $input.groups: + groups=${ str($input.groups).replace(",","-") }, + #end if + #if $input.calc: + calc=${ str($input.calc).replace(",","-") }, + #end if + #elif $input.source == "column": + column=input_dist.dat, + name=input_name.dat, + #elif $input.source == "phylip": + phylip=input_dist.dat, + #end if + #if $count: + count=count.dat, + #end if + fontsize=$fontsize + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <conditional name="input"> + <param name="source" type="select" label="Generate Heatmap for"> + <option value="shared">shared - Sample Similarity - OTU Shared</option> + <option value="phylip">phylip - Phylip Distance Matrix</option> + <option value="column">colomn - Pairwise Column Distance Matrix</option> + </param> + <when value="shared"> + <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> + <param name="label" type="select" label="label - OTU Labels" multiple="true"> + <expand macro="labeloptions"/> + </param> + <param name="groups" type="select" multiple="true" label="groups - Groups to include"> + <options> + <filter type="data_meta" ref="otu" key="groups"/> + </options> + </param> + <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)"> + <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> + <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> + <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> + <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> + <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option> + <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> + <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option> + <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> + <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> + <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> + </param> + </when> + <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 - Names"/> + </when> + <when value="phylip"> + <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> + </when> + </conditional> + <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/> + <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="heatmap" format="svg" from_work_dir="input_dist*.heatmap.sim.svg" label="${tool.name} on ${on_string}: heatmap.sim.svg"> + <filter>input['source'] != 'shared'</filter> + </data> + <collection name="heatmaps" type="list" label="${tool.name} on ${on_string}: Heatmaps"> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.sim\.svg"/> + <filter>input['source'] == 'shared'</filter> + </collection> + </outputs> + <tests> + <test> + <param name="source" value="phylip"/> + <param name="dist" value="amazon.dist" ftype="mothur.square.dist"/> + <output name="heatmap"> + <assert_contents> + <has_text text="svg xmlns:svg="/> + <has_text text="Heatmap for"/> + <has_text text="U68640"/> + </assert_contents> + </output> + <expand macro="logfile-test"/> + </test> + <test> + <param name="source" value="shared"/> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <output_collection name="heatmaps" count="72"> + <element name="0.55.jest.heatmap" md5="c48bac26a84f657ead8dd43af0401317"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test> + <param name="source" value="shared"/> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="label" value="0.03,0.26,0.55"/> + <param name="calc" value="jclass,jest,sorclass,sorest,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc"/> + <param name="groups" value="forest,pasture"/> + <output_collection name="heatmaps" count="30"> + <element name="0.03.braycurtis.heatmap" md5="6a3f261e1012edaf620f78b62eff5c88"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The heatmap.sim_ command generates a heat map from data provided in either a shared_ file, a phylip_ distance matrix, or a column_ distance matrix and a name_ file. For calc parameter choices see: https://www.mothur.org/wiki/Calculators + +.. _shared: https://www.mothur.org/wiki/Shared_file +.. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix +.. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix +.. _name: https://www.mothur.org/wiki/Name_file +.. _heatmap.sim: https://www.mothur.org/wiki/Heatmap.sim + +v.1.24.0: Updated to Mothur 1.33, added count parameter +]]> + </help> + <expand macro="citations"/> +</tool>