Mercurial > repos > bgruening > deeptools

changeset 22:8710187d1eb5 draft

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Uploaded
author bgruening
date Thu, 12 Dec 2013 18:11:46 -0500
parents 8436c195dd6c
children b8ba675a5895
files bamCompare.xml bamCorrelate.xml bamCoverage.xml bamFingerprint.xml bigwigCompare.xml computeGCBias.xml computeMatrix.xml correctGCBias.xml deepTools_macros.xml heatmapper.xml profiler.xml
diffstat 11 files changed, 84 insertions(+), 90 deletions(-) [+]
line wrap: on
line diff
--- a/bamCompare.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/bamCompare.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -1,6 +1,7 @@
 <tool id="deeptools_bamCompare" name="bamCompare" version="1.0">
     <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
     <expand macro="requirements" />
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
--- a/bamCorrelate.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/bamCorrelate.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -1,6 +1,7 @@
 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.1">
     <description>correlates pairs of BAM files</description>
     <expand macro="requirements" />
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
--- a/bamCoverage.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/bamCoverage.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -1,6 +1,7 @@
 <tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0">
     <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
     <expand macro="requirements" />
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
--- a/bamFingerprint.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/bamFingerprint.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -1,6 +1,7 @@
 <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0">
     <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
     <expand macro="requirements" />
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
--- a/bigwigCompare.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/bigwigCompare.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -1,6 +1,7 @@
 <tool id="deeptools_bigwigCompare" name="bigwigCompare" version="1.0">
     <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description>
     <expand macro="requirements"/>
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
@@ -29,10 +30,6 @@
 
         #end if
     </command>
-    <stdio>
-        <regex match="Error:" />
-        <regex match="EXception:" />
-    </stdio>
     <inputs>
         <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
         <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" />
--- a/computeGCBias.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/computeGCBias.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -1,9 +1,7 @@
 <tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.1">
     <description>to see whether your samples should be normalized for GC bias</description>
     <expand macro="requirements" />
-    <stdio>
-        <exit_code range="0" level="warning" description="Warning" />
-    </stdio>
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
--- a/computeMatrix.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/computeMatrix.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -1,6 +1,7 @@
 <tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0">
     <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
     <expand macro="requirements" />
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
@@ -116,7 +117,7 @@
       <when value="reference-point">
         <param name="referencePoint" type="select" label="The reference point for the plotting">
             <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>
-            <option value="TES">end of region (e.g. TES)</option>
+            <option	 value="TES">end of region (e.g. TES)</option>
             <option value="center">center of region</option>
         </param>
         
@@ -126,19 +127,8 @@
         <param name="afterRegionStartLength" type="integer" value="1000" min="1" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/>
       </when>
     </conditional>
-    
-    <conditional name="output" >
-        <param name="showOutputSettings" type="select" label="Show additional output options" >
-            <option value="no" selected="true">no</option>
-            <option value="yes">yes</option>
-        </param>
-          <when value="no" />
-          <when value="yes">
-            <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/>
-            <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/>
-            <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping 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."/>
-        </when>
-    </conditional>
+
+    <expand macro="graphic_output_settings" />
 
     <conditional name="advancedOpt" >
       <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -183,32 +173,8 @@
     
     </inputs>
   <outputs>
-    <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix">
-    </data>
-    <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
-        <filter>
-        ((
-            output['showOutputSettings'] == 'yes' and 
-            output['saveData'] is True
-        ))
-        </filter>
-    </data>
-    <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
-        <filter>
-        ((
-            output['showOutputSettings'] == 'yes' and 
-            output['saveMatrix'] is True
-        ))
-        </filter>
-    </data>
-    <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
-        <filter>
-        ((
-            output['showOutputSettings'] == 'yes' and 
-            output['saveSortedRegions'] is True
-        ))
-        </filter>
-    </data>
+    <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
+    <expand macro="output_graphic_outputs" />
   </outputs>
     <!--
     computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 
--- a/correctGCBias.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/correctGCBias.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -1,6 +1,7 @@
 <tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.1">
     <description>uses the output from computeGCBias to generate corrected BAM files</description>
     <expand macro="requirements" />
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
--- a/deepTools_macros.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/deepTools_macros.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -47,13 +47,23 @@
             <requirement type="package" version="0.1">ucsc_tools</requirement>
             <requirement type="package" version="1.7.1">numpy</requirement>
             <requirement type="package" version="0.7.7">pysam</requirement>
+            <requirement type="package" version="0.12.0">scipy</requirement>
             <requirement type="package" version="1.2.1">matplotlib</requirement>
             <requirement type="package" version="0.1.19">samtools</requirement>
             <requirement type="package" version="12-2013">bx-python</requirement>
             <yield />
         </requirements>
-        </macro>
-
+    </macro>
+    <macro name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+            <exit_code range="0" level="warning" description="Warning" />
+            <regex match="Error:" />
+            <regex match="Exception:" />
+            <regex match="EXception:" />
+        </stdio>
+    </macro>
     <token name="@REFERENCES@">
 
 For more informations, please visit our `project site`_.
@@ -144,6 +154,16 @@
         </conditional>
     </macro>
 
+    <macro name="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="graphic_output_settings">
         <conditional name="output" >
             <param name="showOutputSettings" type="select" label="Show advanced output settings" >
@@ -152,13 +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."/>
@@ -166,8 +180,34 @@
         </conditional>
     </macro>
 
+    <macro name="output_graphic_outputs">
+        <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and 
+                output['saveData'] is True
+            ))
+            </filter>
+        </data>
+        <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and 
+                output['saveMatrix'] is True
+            ))
+            </filter>
+        </data>
+        <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and 
+                output['saveSortedRegions'] is True
+            ))
+            </filter>
+        </data>
+    </macros>
+
     <macro name="colormap">
-
         <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
             <option value="RdYlBu" selected="true">RdYlBu</option>
             <option value="Accent">Accent</option>
--- a/heatmapper.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/heatmapper.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -1,10 +1,7 @@
 <tool id="deeptools_heatmapper" name="heatmapper" version="1.0">
     <description>creates a heatmap for a score associated to genomic regions</description>
-    <expand macro="requirements">
-        <requirement type="package" version="1.7.1">numpy</requirement>
-        <requirement type="package" version="1.2.1">matplotlib</requirement>
-        <requirement type="package" version="0.12.0">scipy</requirement>
-    </expand>
+    <expand macro="requirements"/>
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
@@ -89,7 +86,9 @@
   <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="image_file_format" />
+    <expand>
 
     <conditional name="advancedOpt" >
       <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -162,22 +161,16 @@
   </inputs>
   <outputs>
     <data format="png" name="outFileName" label="${tool.name} image">
-    <change_format>
-        <when input="output.outFileFormat" value="pdf" format="pdf" />
-        <when input="output.outFileFormat" value="svg" format="svg" />
-        <when input="output.outFileFormat" value="eps" format="eps" />
-        <when input="output.outFileFormat" value="emf" format="emf" />
-    </change_format>
+        <change_format>
+            <when input="output.outFileFormat" value="pdf" format="pdf" />
+            <when input="output.outFileFormat" value="svg" format="svg" />
+            <when input="output.outFileFormat" value="eps" format="eps" />
+            <when input="output.outFileFormat" value="emf" format="emf" />
+        </change_format>
     </data>
-    <data format="tabular" name="outFileNameData" label="${tool.name} raw plot data">
-      <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter>
-    </data>
-    <data format="tabular" name="outFileNameMatrix" label="${tool.name} matrix of heatmap values">
-      <filter>(output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)</filter>
-    </data>
-    <data format="bed" name="outFileSortedRegions" label="${tool.name} sorted/filtered regions">
-      <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter>
-    </data>  
+
+    <expand macro="output_graphic_outputs" />
+
   </outputs>
     <tests>
         <test>
--- a/profiler.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/profiler.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -3,6 +3,7 @@
         creates a profile plot for a score associated to genomic regions
     </description>
     <expand macro="requirements" />
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
@@ -80,7 +81,9 @@
             </when>
         </conditional>
 
-        <expand macro="graphic_output_settings" />
+        <expand macro="graphic_output_settings">
+            <expand macro="image_file_format" />
+        <expand>
 
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -130,17 +133,9 @@
                 <when input="output.outFileFormat" value="emf" format="emf" />
             </change_format>
         </data>
-        <data format="tabular" name="outFileNameData" label="${tool.name} raw plot data">
-            <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter>
-        </data>
-        <data format="tabular" name="outFileNameMatrix" label="${tool.name} matrix of heatmap values">
-            <filter>(output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)</filter>
-        </data>
-        <data format="bed" name="outFileSortedRegions" label="${tool.name} sorted/filtered regions">
-            <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter>
-        </data>
-  </outputs>
-  <help>
+        <expand macro="output_graphic_outputs" />
+    </outputs>
+    <help>
 
 **What it does**