Mercurial > repos > bgruening > deeptools

changeset 11:baf4283e2d7f draft

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Uploaded
author bgruening
date Sat, 14 Dec 2013 07:00:55 -0500
parents 135f3bae5c56
children aea72b24dea0
files bamCorrelate.xml deepTools_macros.xml heatmapper.xml profiler.xml
diffstat 4 files changed, 29 insertions(+), 36 deletions(-) [+]
line wrap: on
line diff
--- a/bamCorrelate.xml	Sat Dec 14 03:29:29 2013 -0500
+++ b/bamCorrelate.xml	Sat Dec 14 07:00:55 2013 -0500
@@ -107,13 +107,7 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="outFileFormat" type="select" label="Image file format">
-                    <option value="png" selected="true">png</option>
-                    <option value="pdf">pdf</option>
-                    <option value="svg">svg</option>
-                    <option value="eps">eps</option>
-                    <option value="emf">emf</option>
-                </param>
+                <expand macro="input_image_file_format"/>
                 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
                 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
             </when>
@@ -121,14 +115,7 @@
 
     </inputs>
     <outputs>
-        <data format="png" name="outFileName">
-            <change_format>
-                <when input="output.outFileFormat" value="pdf" format="pdf" />
-                <when input="output.outFileFormat" value="svg" format="svg" />
-                <when input="output.outFileFormat" value="eps" format="eps" />
-                <when input="output.outFileFormat" value="emf" format="emf" />
-            </change_format>
-        </data>
+        <expand macro="output_image_file_format" />
         <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
             <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveRawCounts'] == True)</filter>
         </data>
--- a/deepTools_macros.xml	Sat Dec 14 03:29:29 2013 -0500
+++ b/deepTools_macros.xml	Sat Dec 14 07:00:55 2013 -0500
@@ -172,13 +172,7 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="outFileFormat" type="select" label="Image file format">
-                    <option value="png" selected="true">png</option>
-                    <option value="pdf">pdf</option>
-                    <option value="svg">svg</option>
-                    <option value="eps">eps</option>
-                    <option value="emf">emf</option>
-                </param>
+                <yield />
                 <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/>
                 <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/>
                 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
@@ -186,7 +180,17 @@
         </conditional>
     </macro>
 
-    <macro name="output_graphic_outputs">
+    <macro name="input_image_file_format">
+        <param name="outFileFormat" type="select" label="Image file format">
+            <option value="png" selected="true">png</option>
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+            <option value="eps">eps</option>
+            <option value="emf">emf</option>
+        </param>
+    </macro>
+
+    <macro name="output_image_file_format">
         <data format="png" name="outFileName" label="${tool.name} image">
             <change_format>
                 <when input="output.outFileFormat" value="pdf" format="pdf" />
@@ -195,6 +199,10 @@
                 <when input="output.outFileFormat" value="emf" format="emf" />
             </change_format>
         </data>
+    </macro>
+
+    <macro name="output_graphic_outputs">
+        <yield />
         <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
             <filter>
             ((
--- a/heatmapper.xml	Sat Dec 14 03:29:29 2013 -0500
+++ b/heatmapper.xml	Sat Dec 14 07:00:55 2013 -0500
@@ -84,7 +84,9 @@
     <inputs>
         <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
 
-        <expand macro="graphic_output_settings" />
+        <expand macro="graphic_output_settings">
+            <expand macro="input_image_file_format" />
+        </expand>
 
         <conditional name="advancedOpt" >
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -153,15 +155,9 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="png" name="outFileName" label="${tool.name} image">
-            <change_format>
-                <when input="output.outFileFormat" value="pdf" format="pdf" />
-                <when input="output.outFileFormat" value="svg" format="svg" />
-                <when input="output.outFileFormat" value="eps" format="eps" />
-                <when input="output.outFileFormat" value="emf" format="emf" />
-            </change_format>
-        </data>
-        <expand macro="output_graphic_outputs" />
+        <expand macro="output_graphic_outputs">
+            <expand macro="output_image_file_format" />
+        </expand>
     </outputs>
     <tests>
         <test>
--- a/profiler.xml	Sat Dec 14 03:29:29 2013 -0500
+++ b/profiler.xml	Sat Dec 14 07:00:55 2013 -0500
@@ -80,8 +80,8 @@
         </conditional>
 
         <expand macro="graphic_output_settings">
-            <expand macro="image_file_format" />
-        <expand>
+            <expand macro="input_image_file_format" />
+        </expand>
 
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -122,7 +122,9 @@
         </conditional>
     </inputs>
     <outputs>
-        <expand macro="output_graphic_outputs" />
+        <expand macro="output_graphic_outputs">
+            <expand macro="output_image_file_format" />
+        </expand>
     </outputs>
     <help>