Mercurial > repos > iuc > mothur_heatmap_bin
view heatmap.bin.xml @ 3:ac3f8a1a3e43 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746
author | iuc |
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date | Fri, 06 Apr 2018 04:28:46 -0400 |
parents | ac2fa6a167ad |
children | 35a719cd08da |
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<tool profile="16.07" id="mothur_heatmap_bin" name="Heatmap.bin" version="@WRAPPER_VERSION@.0"> <description>Generate a heatmap for OTUs</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.otu' input_otu.dat && echo 'heatmap.bin( #if $input.otu.is_of_type("mothur.rabund"): rabund=input_otu.dat, #elif $input.otu.is_of_type("mothur.sabund"): sabund=input_otu.dat, #elif $input.otu.is_of_type("mothur.list"): list=input_otu.dat, #elif $input.otu.is_of_type("mothur.relabund"): relabund=input_otu.dat, #elif $input.otu.is_of_type("mothur.shared"): shared=input_otu.dat, #end if #if $input.has_groups == 'yes' and $input.groups: groups=${ str($input.groups).replace(",","-") }, #end if #if $input.label: label=${ str($input.label).replace(",","-") }, #end if scale=$scale, sorted=$sorted, numotu=$numotu, fontsize=$fontsize )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <conditional name="input"> <param name="has_groups" type="select" label="Generate Heatmap for"> <option value="no">list, rabund, sabund</option> <option value="yes">shared, relabund</option> </param> <when value="no"> <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund" label="list,rabund,sabund - OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <expand macro="labeloptions"/> </param> </when> <when value="yes"> <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund file - OTU List"/> <param name="groups" type="select" multiple="true" label="groups - Groups to include"> <options> <filter type="data_meta" ref="otu" key="groups"/> </options> </param> <param name="label" type="select" multiple="true" label="label - OTU Labels"> <expand macro="labeloptions"/> </param> </when> </conditional> <param name="scale" type="select" label="scale - Scaling for heatmap"> <option value="log10" selected="true">Log10</option> <option value="log2">Log2</option> <option value="linear">Linear</option> </param> <param name="sorted" type="select" label="sorted - Sort heatmap"> <option value="shared" selected="true">By shared</option> <option value="none">Don't sort</option> <option value="topotu">By Total OTUs</option> <option value="topgroup">By Total Groups</option> </param> <param name="numotu" type="integer" value="0" min="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/> <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <collection name="heatmaps" type="list" label="${tool.name} on ${on_string}: Heatmaps"> <discover_datasets pattern=".*?\.(?P<designation>.*)\.bin\.svg"/> </collection> </outputs> <tests> <test> <param name="otu" value="amazon.an.list" ftype="mothur.list"/> <param name="has_groups" value="no"/> <output_collection name="heatmaps" count="36"> <element name="0.26.heatmap" md5="8f0d5cb95808115e50729e6df60629cc"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/> <param name="has_groups" value="yes"/> <param name="groups" value="forest"/> <param name="label" value="0.26"/> <output_collection name="heatmaps" count="1"> <element name="0.26.heatmap" md5="b2b46b7e55f55e2b260cd6dc6ccb4485"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> <param name="has_groups" value="yes"/> <param name="label" value="0.03,0.26,0.55"/> <param name="groups" value="forest,pasture"/> <param name="fontsize" value="100"/> <param name="scale" value="linear"/> <param name="sorted" value="none"/> <output_collection name="heatmaps" count="3"> <element name="0.26.heatmap" md5="b46ed47e441a30588f60e1554ff703bb"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The heatmap.bin_ command generates a heat map from data provided in either a list_ or a shared_ file. .. _list: https://www.mothur.org/wiki/List_file .. _shared: https://www.mothur.org/wiki/Shared_file .. _heatmap.bin: https://www.mothur.org/wiki/Heatmap.bin v.1.21.0: Updated to Mothur 1.33 ]]></help> <expand macro="citations"/> </tool>