From 45cbe52e4943ad2b00ebd6c3b7b969aa05bc2683 Mon Sep 17 00:00:00 2001
From: tbrown91 <brown@izw-berlin.de>
Date: Wed, 27 Mar 2024 10:58:23 +0100
Subject: [PATCH 1/7] Initial add cooler zoomify

---
 tools/cooler/cooler_zoomify.xml     |  47 ++++++++++++++++++++++++++++
 tools/cooler/test-data/input.mcool  | Bin 0 -> 43560 bytes
 tools/cooler/test-data/output.mcool | Bin 0 -> 43560 bytes
 3 files changed, 47 insertions(+)
 create mode 100644 tools/cooler/cooler_zoomify.xml
 create mode 100644 tools/cooler/test-data/input.mcool
 create mode 100644 tools/cooler/test-data/output.mcool

diff --git a/tools/cooler/cooler_zoomify.xml b/tools/cooler/cooler_zoomify.xml
new file mode 100644
index 0000000..48cfca0
--- /dev/null
+++ b/tools/cooler/cooler_zoomify.xml
@@ -0,0 +1,47 @@
+<tool id="cooler_zoomify" name="cooler_zoomify" version="@VERSION@+galaxy0" profile="18.01">
+  <description>Copy and balance a cool file.</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+  <command detect_errors="exit_code"><![CDATA[
+    cooler zoomify -p \${GALAXY_SLOTS:-4}
+    -c $chunksize
+    -r '$resolution'
+    -o '$output'
+    '$input'
+    ]]>
+  </command>
+  <inputs>
+    <param name="input" multiple="false" type="data" format="cool" label="Select the input cool file to zoomify."/>
+    <param argument="-c" type="integer" value="10000000" label="Number of pixels dedicated to each process"/>
+    <param argument="-r" type="text" value="B" label="Resultion" help="Comma-separated list of target resolutions. Use suffixes B or N to specify a progression: B for binary (geometric steps of factor 2), N for nice (geometric steps of factor 10 interleaved with steps of 2 and 5). Examples: 1000B=1000,2000,4000,8000,... 1000N=1000,2000,5000,10000,... 5000N=5000,10000,25000,50000,... 4DN is an alias for 1000,2000,5000N">
+        <validator type="regex">[BDN0-9,]+</validator>
+        </param>
+  </inputs>
+  
+  <outputs>
+    <data type="data" format="mcool" name="output" label="Multi-resolution mcool file from $input.name"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="input" value="input.cool" ftype="cool"/>
+      <output name="output" file="output.mcool" compare="sim_size"/>
+    </test>
+  </tests> 
+
+  <help>
+    **cooler zoomify**
+    tool developped by mirnylab
+    see https://github.com/mirnylab/cooler
+    and https://cooler.readthedocs.io/en/latest/cli.html#cooler-balance
+    
+    command-line::
+    
+      cooler zoomify -p \${GALAXY_SLOTS:-1} -c $chunksize -r '$resolution'
+    
+  </help>
+  <expand macro="citation_cooler" />
+</tool>
diff --git a/tools/cooler/test-data/input.mcool b/tools/cooler/test-data/input.mcool
new file mode 100644
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diff --git a/tools/cooler/test-data/output.mcool b/tools/cooler/test-data/output.mcool
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HcmV?d00001


From cffc19acbcd7fc94cf73e8ea4767eb6441f523d9 Mon Sep 17 00:00:00 2001
From: tbrown91 <brown@izw-berlin.de>
Date: Wed, 27 Mar 2024 16:32:11 +0100
Subject: [PATCH 2/7] Corrected parameter variables and descriptive text

---
 tools/cooler/cooler_zoomify.xml | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/tools/cooler/cooler_zoomify.xml b/tools/cooler/cooler_zoomify.xml
index 48cfca0..293929d 100644
--- a/tools/cooler/cooler_zoomify.xml
+++ b/tools/cooler/cooler_zoomify.xml
@@ -1,5 +1,5 @@
-<tool id="cooler_zoomify" name="cooler_zoomify" version="@VERSION@+galaxy0" profile="18.01">
-  <description>Copy and balance a cool file.</description>
+<tool id="cooler_zoomify" name="Cooler zoomify" version="@VERSION@+galaxy0" profile="18.01">
+  <description>Generate a multi-resolution cooler file by coarsening</description>
   <macros>
     <import>macros.xml</import>
   </macros>
@@ -7,8 +7,8 @@
   <expand macro="stdio" />
   <command detect_errors="exit_code"><![CDATA[
     cooler zoomify -p \${GALAXY_SLOTS:-4}
-    -c $chunksize
-    -r '$resolution'
+    -c $c
+    -r $r
     -o '$output'
     '$input'
     ]]>
@@ -34,14 +34,8 @@
 
   <help>
     **cooler zoomify**
-    tool developped by mirnylab
-    see https://github.com/mirnylab/cooler
-    and https://cooler.readthedocs.io/en/latest/cli.html#cooler-balance
-    
-    command-line::
-    
-      cooler zoomify -p \${GALAXY_SLOTS:-1} -c $chunksize -r '$resolution'
-    
+    Generate a multi-resolution cooler file by coarsening
+    Given a set of resolutions, generate a multi-cooler file from a cooler for visualisation with higlass.
   </help>
   <expand macro="citation_cooler" />
 </tool>

From c134f8013fd37ea56df6b426911e284df3e560bb Mon Sep 17 00:00:00 2001
From: tbrown91 <brown@izw-berlin.de>
Date: Thu, 28 Mar 2024 13:12:36 +0100
Subject: [PATCH 3/7] Added output filetype in test

---
 tools/cooler/cooler_zoomify.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/cooler/cooler_zoomify.xml b/tools/cooler/cooler_zoomify.xml
index 293929d..eff2414 100644
--- a/tools/cooler/cooler_zoomify.xml
+++ b/tools/cooler/cooler_zoomify.xml
@@ -28,7 +28,7 @@
   <tests>
     <test>
       <param name="input" value="input.cool" ftype="cool"/>
-      <output name="output" file="output.mcool" compare="sim_size"/>
+      <output name="output" file="output.mcool" ftype="mcool" compare="sim_size"/>
     </test>
   </tests> 
 

From e179fafca60484cf81bf51a805b32ebe8c18ae53 Mon Sep 17 00:00:00 2001
From: tbrown91 <brown@izw-berlin.de>
Date: Thu, 28 Mar 2024 13:21:01 +0100
Subject: [PATCH 4/7] Corrected output data format

---
 tools/cooler/cooler_zoomify.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/cooler/cooler_zoomify.xml b/tools/cooler/cooler_zoomify.xml
index eff2414..69a94bb 100644
--- a/tools/cooler/cooler_zoomify.xml
+++ b/tools/cooler/cooler_zoomify.xml
@@ -14,7 +14,7 @@
     ]]>
   </command>
   <inputs>
-    <param name="input" multiple="false" type="data" format="cool" label="Select the input cool file to zoomify."/>
+    <param name="input" multiple="false" type="data" format="cool" label="Select the input cool file to zoomify"/> 
     <param argument="-c" type="integer" value="10000000" label="Number of pixels dedicated to each process"/>
     <param argument="-r" type="text" value="B" label="Resultion" help="Comma-separated list of target resolutions. Use suffixes B or N to specify a progression: B for binary (geometric steps of factor 2), N for nice (geometric steps of factor 10 interleaved with steps of 2 and 5). Examples: 1000B=1000,2000,4000,8000,... 1000N=1000,2000,5000,10000,... 5000N=5000,10000,25000,50000,... 4DN is an alias for 1000,2000,5000N">
         <validator type="regex">[BDN0-9,]+</validator>
@@ -22,7 +22,7 @@
   </inputs>
   
   <outputs>
-    <data type="data" format="mcool" name="output" label="Multi-resolution mcool file from $input.name"/>
+    <data format="mcool" name="output" label="Multi-resolution mcool file from $input.name"/>
   </outputs>
   
   <tests>

From f44ed07eca373423717116fda85765d3881d0622 Mon Sep 17 00:00:00 2001
From: tbrown91 <brown@izw-berlin.de>
Date: Thu, 28 Mar 2024 15:26:28 +0100
Subject: [PATCH 5/7] Corrected input text

---
 tools/cooler/cooler_zoomify.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/cooler/cooler_zoomify.xml b/tools/cooler/cooler_zoomify.xml
index 69a94bb..8988f85 100644
--- a/tools/cooler/cooler_zoomify.xml
+++ b/tools/cooler/cooler_zoomify.xml
@@ -8,7 +8,7 @@
   <command detect_errors="exit_code"><![CDATA[
     cooler zoomify -p \${GALAXY_SLOTS:-4}
     -c $c
-    -r $r
+    -r '$r'
     -o '$output'
     '$input'
     ]]>

From 1c052fbf13e4b57f63f1fa8034eb511598bbf460 Mon Sep 17 00:00:00 2001
From: tbrown91 <brown@izw-berlin.de>
Date: Thu, 28 Mar 2024 15:49:27 +0100
Subject: [PATCH 6/7] removed superfluous file

---
 tools/cooler/test-data/input.mcool | Bin 43560 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 tools/cooler/test-data/input.mcool

diff --git a/tools/cooler/test-data/input.mcool b/tools/cooler/test-data/input.mcool
deleted file mode 100644
index 42cdfbad1cd70815dc91a996b3b52dae31e975e7..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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From 3b0c1295fe657ce2bf4b7ab6a14b3f0287d8f904 Mon Sep 17 00:00:00 2001
From: tbrown91 <brown@izw-berlin.de>
Date: Mon, 1 Apr 2024 10:40:32 +0200
Subject: [PATCH 7/7] zoomify output tests

---
 tools/cooler/cooler_zoomify.xml     |   1 +
 tools/cooler/test-data/output.mcool | Bin 43560 -> 120507 bytes
 2 files changed, 1 insertion(+)

diff --git a/tools/cooler/cooler_zoomify.xml b/tools/cooler/cooler_zoomify.xml
index 8988f85..e5b582d 100644
--- a/tools/cooler/cooler_zoomify.xml
+++ b/tools/cooler/cooler_zoomify.xml
@@ -29,6 +29,7 @@
     <test>
       <param name="input" value="input.cool" ftype="cool"/>
       <output name="output" file="output.mcool" ftype="mcool" compare="sim_size"/>
+      <param name="r" value="1000000,2000000,4000000"/>
     </test>
   </tests> 
 
diff --git a/tools/cooler/test-data/output.mcool b/tools/cooler/test-data/output.mcool
index 42cdfbad1cd70815dc91a996b3b52dae31e975e7..4014aba5f2cf47478892c0cc371642d21ce25770 100644
GIT binary patch
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