Mercurial > repos > iuc > mothur_heatmap_sim
diff heatmap.sim.xml @ 1:4c752399b0c7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 18:15:19 -0400 |
| parents | edf78e2b71d4 |
| children | eb3fcb541aad |
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--- a/heatmap.sim.xml Fri Jun 24 16:35:34 2016 -0400 +++ b/heatmap.sim.xml Thu May 18 18:15:19 2017 -0400 @@ -4,8 +4,11 @@ <import>macros.xml</import> </macros> <expand macro="requirements"/> + <expand macro="stdio"/> <expand macro="version_command"/> - <command detect_errors="aggressive"><![CDATA[ + <command><![CDATA[ + @SHELL_OPTIONS@ + ## create symlinks to input datasets ln -s "$count" count.dat && #if $input.source == 'shared': @@ -42,6 +45,7 @@ )' | sed 's/ //g' ## mothur trips over whitespace | mothur + | tee mothur.out.log ]]></command> <inputs> <conditional name="input"> @@ -78,7 +82,7 @@ <param name="name" type="data" format="mothur.names" label="name - Names"/> </when> <when value="phylip"> - <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> + <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)"/> @@ -132,15 +136,15 @@ @MOTHUR_OVERVIEW@ -**Command Documenation** +**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: http://www.mothur.org/wiki/Calculators +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: http://www.mothur.org/wiki/Shared_file -.. _phylip: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix -.. _column: http://www.mothur.org/wiki/Column-formatted_distance_matrix -.. _name: http://www.mothur.org/wiki/Name_file -.. _heatmap.sim: http://www.mothur.org/wiki/Heatmap.sim +.. _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 ]]>