Mercurial > repos > bgruening > deeptools_plot_pca

changeset 21:93ce2662f917 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a
author bgruening
date Wed, 22 Aug 2018 17:00:56 -0400
parents aca788d8e71d
children 432443fa7765
files deepTools_macros.xml plotPCA.xml test-data/plotPCA_result1.png test-data/plotPCA_result2.png
diffstat 4 files changed, 12 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/deepTools_macros.xml	Mon Jul 09 18:41:04 2018 -0400
+++ b/deepTools_macros.xml	Wed Aug 22 17:00:56 2018 -0400
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.1.0</token>
+    <token name="@WRAPPER_VERSION@">3.1.2.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.1.0">deeptools</requirement>
+            <requirement type="package" version="3.1.2">deeptools</requirement>
             <requirement type="package" version="1.7">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -216,7 +216,7 @@
             label="Use a metagene model"
             help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
         <param argument="--transcriptID" optional="True" value="transcript" type="text"
-            label="trascript designator"
+            label="transcript designator"
             help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
         <param argument="--exonID" optional="True" value="exon" type="text"
             label="exon designator"
@@ -654,7 +654,7 @@
     </xml>
 
     <xml name="output_image_file_format">
-        <data format="png" name="outFileName" label="${tool.name} image">
+        <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
             <change_format>
                 <when input="output.outFileFormat" value="pdf" format="pdf" />
                 <when input="output.outFileFormat" value="svg" format="svg" />
@@ -665,7 +665,7 @@
     </xml>
 
     <xml name="output_image_file_format_not_nested">
-        <data format="png" name="outFileName" label="${tool.name} image">
+        <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
             <change_format>
                 <when input="outFileFormat" value="pdf" format="pdf" />
                 <when input="outFileFormat" value="svg" format="svg" />
--- 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>
Binary file test-data/plotPCA_result1.png has changed
Binary file test-data/plotPCA_result2.png has changed