From 4d9438e7ef0843976f330884ac3d331258b30271 Mon Sep 17 00:00:00 2001
From: npinter <npinter@protonmail.com>
Date: Tue, 27 Feb 2024 10:37:24 +0100
Subject: [PATCH 1/3] Fix outputs section

---
 tools/peakzilla/peakzilla.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/peakzilla/peakzilla.xml b/tools/peakzilla/peakzilla.xml
index d302018c582..452d2aadaad 100644
--- a/tools/peakzilla/peakzilla.xml
+++ b/tools/peakzilla/peakzilla.xml
@@ -2,7 +2,7 @@
     <description>Identify transcription factor binding sites from ChIP-seq and ChIP-exo experiments</description>
     <macros>
         <token name="@TOOL_VERSION@">1.0</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="2.7">python</requirement>
@@ -63,10 +63,10 @@
     <outputs>
         <data name="results" format="tabular" label="${tool.name} on ${on_string}"/>
         <data name="log" format="txt" from_work_dir="log.txt" label="Log file for ${tool.name} on ${on_string}">
-            <filter>log</filter>
+            <filter>outputs["log"]</filter>
         </data>
         <data name="negative_peaks" format="tabular" from_work_dir="negative_peaks.tsv" label="Negative peaks for ${tool.name} on ${on_string}">
-            <filter>negative</filter>
+            <filter>outputs["negative"]</filter>
         </data>
     </outputs>
     <tests>

From 8c8ac03562e7ec1b2afdad5b497689b5c0db5f8b Mon Sep 17 00:00:00 2001
From: npinter <npinter@protonmail.com>
Date: Tue, 27 Feb 2024 10:49:31 +0100
Subject: [PATCH 2/3] Add simple test

---
 tools/peakzilla/peakzilla.xml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/tools/peakzilla/peakzilla.xml b/tools/peakzilla/peakzilla.xml
index 452d2aadaad..913c76f90e7 100644
--- a/tools/peakzilla/peakzilla.xml
+++ b/tools/peakzilla/peakzilla.xml
@@ -70,6 +70,15 @@
         </data>
     </outputs>
     <tests>
+        <test expect_num_outputs="1">
+            <param name="chip_bed" value="chip.bed" />
+            <param name="input_bed" value="input.bed" />
+            <output name="results" file="results.tsv">
+                <assert_contents>
+                    <has_text text="Peak_1" />
+                </assert_contents>
+            </output>
+        </test>
         <test expect_num_outputs="3">
             <param name="chip_bed" value="chip.bed" />
             <param name="input_bed" value="input.bed" />

From cee9cd7d22d20bdfc7e4e8e3c4b8cb42f4921e29 Mon Sep 17 00:00:00 2001
From: npinter <npinter@protonmail.com>
Date: Tue, 27 Feb 2024 11:18:58 +0100
Subject: [PATCH 3/3] Add new test-data

---
 tools/peakzilla/peakzilla.xml                 |  4 +--
 tools/peakzilla/test-data/log.txt             | 30 +++++++++----------
 tools/peakzilla/test-data/results_1.tsv       |  3 ++
 .../test-data/{results.tsv => results_2.tsv}  |  0
 4 files changed, 20 insertions(+), 17 deletions(-)
 create mode 100644 tools/peakzilla/test-data/results_1.tsv
 rename tools/peakzilla/test-data/{results.tsv => results_2.tsv} (100%)

diff --git a/tools/peakzilla/peakzilla.xml b/tools/peakzilla/peakzilla.xml
index 913c76f90e7..790da963b1f 100644
--- a/tools/peakzilla/peakzilla.xml
+++ b/tools/peakzilla/peakzilla.xml
@@ -73,7 +73,7 @@
         <test expect_num_outputs="1">
             <param name="chip_bed" value="chip.bed" />
             <param name="input_bed" value="input.bed" />
-            <output name="results" file="results.tsv">
+            <output name="results" file="results_1.tsv">
                 <assert_contents>
                     <has_text text="Peak_1" />
                 </assert_contents>
@@ -88,7 +88,7 @@
             <param name="score_cutoff" value="1" />
             <param name="log" value="true" />
             <param name="negative" value="true" />
-            <output name="results" file="results.tsv">
+            <output name="results" file="results_2.tsv">
                 <assert_contents>
                     <has_text text="Peak_1" />
                 </assert_contents>
diff --git a/tools/peakzilla/test-data/log.txt b/tools/peakzilla/test-data/log.txt
index 2804954943b..fbe8d40515a 100644
--- a/tools/peakzilla/test-data/log.txt
+++ b/tools/peakzilla/test-data/log.txt
@@ -1,15 +1,15 @@
-10:13:55 Loading tags ...
-10:13:55 Tags in IP: 9953
-10:13:55 Tags in control: 9569
-10:13:55 Fragment size was set manually to 50 bp
-10:13:55 Peak size is 101 bp
-10:13:55 Estimating tag distribution using gaussian ...
-10:13:55 Finding peaks in ChIP sample ...
-10:13:55 Finding peaks in control sample ...
-10:13:55 Calculating peak scores ...
-10:13:55 Calculating FDR ...
-10:13:55 1 peaks detected
-10:13:55 Enrichment cutoff: 2.0
-10:13:55 Score cutoff: 1.0
-10:13:55 Writing input peaks to negative_peaks.tsv
-10:13:55 Done!
+11:01:24 Loading tags ...
+11:01:24 Tags in IP: 9953
+11:01:24 Tags in control: 9569
+11:01:24 Fragment size was set manually to 50 bp
+11:01:24 Peak size is 101 bp
+11:01:24 Estimating tag distribution using gaussian ...
+11:01:24 Finding peaks in ChIP sample ...
+11:01:24 Finding peaks in control sample ...
+11:01:24 Calculating peak scores ...
+11:01:24 Calculating FDR ...
+11:01:24 1 peaks detected
+11:01:24 Enrichment cutoff: 2.0
+11:01:24 Score cutoff: 1.0
+11:01:24 Writing input peaks to negative_peaks.tsv
+11:01:24 Done!
diff --git a/tools/peakzilla/test-data/results_1.tsv b/tools/peakzilla/test-data/results_1.tsv
new file mode 100644
index 00000000000..e446c785218
--- /dev/null
+++ b/tools/peakzilla/test-data/results_1.tsv
@@ -0,0 +1,3 @@
+#Chromosome	Start	End	Name	Summit	Score	ChIP	Control	FoldEnrichment	DistributionScore	FDR
+2R	18296016	18296218	Peak_1	18296117	677.90	1729.79	163.82	10.56	0.43	0.00
+2R	19461248	19461450	Peak_2	19461349	2.54	1063.25	104.50	10.17	0.00	0.00
diff --git a/tools/peakzilla/test-data/results.tsv b/tools/peakzilla/test-data/results_2.tsv
similarity index 100%
rename from tools/peakzilla/test-data/results.tsv
rename to tools/peakzilla/test-data/results_2.tsv