From 57a6dbba36f65cd4c463cb9bc95184269d4538fb Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@users.noreply.github.com>
Date: Wed, 15 May 2019 10:39:39 +0200
Subject: [PATCH] Implement #832 (#835)

* Implement #832

* update dti requirement
---
 deeptools/plotEnrichment.py       | 11 ++++++++++-
 galaxy/wrapper/plotEnrichment.xml |  9 +++++++++
 requirements.txt                  |  2 +-
 setup.py                          |  2 +-
 4 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/deeptools/plotEnrichment.py b/deeptools/plotEnrichment.py
index f902c9dce0..adda203a10 100644
--- a/deeptools/plotEnrichment.py
+++ b/deeptools/plotEnrichment.py
@@ -86,6 +86,11 @@ def plot_enrichment_args():
                           type=parserCommon.writableFile,
                           metavar='FILE')
 
+    optional.add_argument('--attributeKey',
+                          help='Instead of deriving labels from the feature column in a GTF file, '
+                          'use the given attribute key, such as gene_biotype. For BED files or '
+                          'entries without the attribute key, None is used as the label.')
+
     optional.add_argument('--labels', '-l',
                           metavar='sample1 sample2',
                           help='User defined labels instead of default labels from '
@@ -495,10 +500,14 @@ def main(args=None):
     if len(args.labels) != len(args.bamfiles):
         sys.exit("Error: The number of labels ({0}) does not match the number of BAM files ({1})!".format(len(args.labels), len(args.bamfiles)))
 
+    # Ensure that if we're given an attributeKey that it's not empty
+    if args.attributeKey and args.attributeKey == "":
+        args.attributeKey = None
+
     global gtf
     if not args.regionLabels and args.smartLabels:
         args.regionLabels = smartLabels(args.BED)
-    gtf = Enrichment(args.BED, keepExons=args.keepExons, labels=args.regionLabels)
+    gtf = Enrichment(args.BED, keepExons=args.keepExons, labels=args.regionLabels, attributeKey=args.attributeKey)
 
     # Get fragment size and chromosome dict
     fhs = [openBam(x) for x in args.bamfiles]
diff --git a/galaxy/wrapper/plotEnrichment.xml b/galaxy/wrapper/plotEnrichment.xml
index 83d903867f..e54f6daf17 100644
--- a/galaxy/wrapper/plotEnrichment.xml
+++ b/galaxy/wrapper/plotEnrichment.xml
@@ -29,6 +29,10 @@
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes"
+                #if $advancedOpt.attributeKey and str($advancedOpt.attributeKey).strip() != "":
+                    --attributeKey '$advancedOpt.attributeKey'
+                #end if
+
                 #if $advancedOpt.labels and str($advancedOpt.labels).strip() != "":
                     --labels $advancedOpt.labels
                 #end if
@@ -84,6 +88,11 @@
         <expand macro="input_image_file_format" />
 
         <expand macro="advancedOpt_scaffold">
+            <param argument="--attributeKey" type="text" size="20" label="Optional attribute key"
+                help="Instead of deriving the feature label from the feature column, use the value of the given
+                attribute key. For example, the gene_biotype. Note that &quot;None&quote; is used for BED files
+                or entries where the attributeKey is not found." />
+
             <param argument="--plotHeight" type="integer" value="20" min="3"
                 label="Plot height"
                 help="Height in cm. The default for the plot height is 20 centimeters. The minimum value is 3 cm." />
diff --git a/requirements.txt b/requirements.txt
index ab3611b523..cb2b61788e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,4 +6,4 @@ py2bit>=0.2.0
 numpydoc>=0.5
 pyBigWig>=0.2.1
 plotly>=2.0.0
-deeptoolsintervals>=0.1.7
+deeptoolsintervals>=0.1.8
diff --git a/setup.py b/setup.py
index ad6256d2ed..5adedc9e72 100755
--- a/setup.py
+++ b/setup.py
@@ -90,7 +90,7 @@ def openREADME():
         "pyBigWig >= 0.2.1",
         "py2bit >= 0.2.0",
         "plotly >= 2.0.0",
-        "deeptoolsintervals >= 0.1.7"
+        "deeptoolsintervals >= 0.1.8"
     ],
     zip_safe=True,
     cmdclass={'sdist': sdist, 'install': install}