diff plotPCA.xml @ 21:93ce2662f917 draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a

--- a/plotPCA.xml	Mon Jul 09 18:41:04 2018 -0400
+++ b/plotPCA.xml	Wed Aug 22 17:00:56 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_plot_pca" name="plotPCA" version="@WRAPPER_VERSION@.0">
+<tool id="deeptools_plot_pca" name="plotPCA" version="@WRAPPER_VERSION@.0" profile="18.01">
     <description>Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output</description>
     <macros>
         <token name="@BINARY@">plotPCA</token>
@@ -22,6 +22,9 @@
                 #if $advancedOpt.colors:
                     --colors $advancedOpt.colors
                 #end if
+                #if $advancedOpt.markers:
+                    --markers $advancedOpt.markers
+                #end if
             #end if
             #if $outFileNameData
                 --outFileNameData '$output_outFileNameData'
@@ -40,7 +43,7 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <expand macro="plotWidthHeight" PLOTWIDTH="5.0" PLOTHEIGHT="10.0" />
+                <expand macro="plotWidthHeight" PLOTWIDTH="10.0" PLOTHEIGHT="10.0" />
                 <param name="PCs" argument="--PCs" label="Principal components to plot" value="1 2" type="text"
                     help="The principal components to plot. If specified, you must provide two different integers, greater than zero, separated by a space. An example (and the default) is '1 2'." />
                 <param name="ntop" argument="--ntop" label="Number of rows to use" value="1000" type="integer"
@@ -50,6 +53,8 @@
                 <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically. This option is not applicable if the PCA is performed on the transposed matrix." truevalue="--rowCenter" falsevalue="" />
                 <param argument="--colors" type="text" name="colors" label="Symbol colors" value="" optional="True"
                     help="A list of colors for the symbols. Color names and html hex string (e.g., #eeff22) are accepted. The color names should be space separated. For example, --colors 'red blue green'. If not specified, the symbols will be given automatic colors." />
+                <param argument="--markers" type="text" name="markers" label="Custom markers" value="" optional="True"
+                    help="A list of markers for the symbols. (e.g., '&lt;','&gt;','o') are accepted. The marker values should be space separated. For example, 's' 'o' 's' 'o'. If not specified, the symbols will be given automatic shapes." />
             </when>
         </conditional>
     </inputs>