Repository 'bandage'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/bandage

Changeset 8:ddddce450736 (2022-11-28)
Previous changeset 7:21e491ad532a (2022-11-01)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 2b3b163bbe36bb648c17c9b0bf808d41d92078c0
modified:
bandage_image.xml
bandage_info.xml
macros.xml
test-data/out.tab
test-data/out_standard.tab
removed:
test-data/gfa.tabular
test-data/out.jpg
test-data/out.png
test-data/out.svg
test-data/out_fontsize.jpg
test-data/out_labels.svg
b
diff -r 21e491ad532a -r ddddce450736 bandage_image.xml
--- a/bandage_image.xml Tue Nov 01 15:09:04 2022 +0000
+++ b/bandage_image.xml Mon Nov 28 08:20:19 2022 +0000
[
@@ -7,10 +7,13 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"> <![CDATA[
+
+ln -s '$input_file' input.gfa &&
+
 @HEADLESS@
 Bandage
     image
-    '$input_file'
+    input.gfa
     'out.$output_format'
     #if $height:
         --height '$height'
@@ -22,13 +25,13 @@
         --fontsize '$fontsize'
     #end if
     #if $nodewidth:
-        --nodewidth '$nodewidth' 
+        --nodewidth '$nodewidth'
     #end if
     $names
     $lengths
     ]]></command>
     <inputs>
-        <param name="input_file" type="data" format="txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/>
+        <param name="input_file" type="data" format="gfa1,gfa2,fastg,txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/>
         <param argument="--height" type="integer" min="1" value="1000" optional="True" label="Image height" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: 1000."/>
         <param argument="--width" type="integer" min="1" optional="True" label="Image width" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: not set."/>
         <param argument="--names" type="boolean" truevalue="--names" falsevalue="" label="Node name labels?"/>
@@ -52,27 +55,43 @@
     </outputs>
     <tests>
         <test><!-- test with default settings -->
-            <param name="input_file" ftype="tabular" value="gfa.tabular"/>
-            <output name="outfile" ftype="jpg" file="out.jpg" compare="sim_size" delta="70000"/>
+            <param name="input_file" ftype="txt" value="bandage_input.txt"/>
+            <output name="outfile" ftype="jpg">
+              <assert_contents>
+                  <has_size value="47168" delta="15000"/>
+              </assert_contents>
+            </output>
         </test>
         <test><!-- test with width and height parameters -->
-            <param name="input_file" ftype="tabular" value="gfa.tabular"/>
+            <param name="input_file" ftype="txt" value="bandage_input.txt"/>
             <param name="height" value="100"/>
             <param name="width" value="100"/>
             <param name="output_format" value="png"/>
-            <output name="outfile" ftype="png" file="out.png" compare="sim_size" delta="120000"/>
+            <output name="outfile" ftype="png">
+              <assert_contents>
+                  <has_size value="2000" delta="1500"/>
+              </assert_contents>
+            </output>
         </test>
         <test><!-- test svg output -->
-            <param name="input_file" ftype="tabular" value="gfa.tabular"/>
+            <param name="input_file" ftype="txt" value="bandage_input.txt"/>
             <param name="output_format" value="svg"/>
-            <output name="outfile" ftype="svg" file="out.svg" compare="sim_size" delta="120000"/>
+            <output name="outfile" ftype="svg">
+              <assert_contents>
+                  <has_size value="15154" delta="5000"/>
+              </assert_contents>
+            </output>
         </test>
         <test><!-- test with node name and length labels -->
-            <param name="input_file" ftype="txt" value="gfa.tabular"/>
+            <param name="input_file" ftype="txt" value="bandage_input.txt"/>
             <param name="output_format" value="svg"/>
             <param name="names" value="--names"/>
             <param name="lengths" value="--lengths"/>
-            <output name="outfile" ftype="svg" file="out_labels.svg" compare="sim_size" delta="250000"/>
+            <output name="outfile" ftype="svg">
+              <assert_contents>
+                  <has_size value="49566" delta="15000"/>
+              </assert_contents>
+            </output>
         </test>
         <test><!-- test with node name, length labels and fontsize-->
             <param name="input_file" ftype="txt" value="bandage_input.txt"/>
@@ -80,10 +99,17 @@
             <param name="names" value="--names"/>
             <param name="lengths" value="--lengths"/>
             <param name="fontsize" value="5"/>
-            <output name="outfile" ftype="jpg" file="out_fontsize.jpg" compare="sim_size" delta="250000"/>
+            <output name="outfile" ftype="jpg">
+              <assert_contents>
+                  <has_size value="45286" delta="15000"/>
+              </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
+
+*THE NEW BANDAGE: As of version 2022.09, the Bandage tool is now built on `Bandage-NG <https://github.com/asl/BandageNG>`_. This fork of the original Bandage is better maintained with additional features and performance upgrades.*
+
 @BANDAGE_OVERVIEW@
 
 **Command Documentation**
@@ -96,4 +122,3 @@
     ]]></help>
     <expand macro="citations"/>
 </tool>
-
b
diff -r 21e491ad532a -r ddddce450736 bandage_info.xml
--- a/bandage_info.xml Tue Nov 01 15:09:04 2022 +0000
+++ b/bandage_info.xml Mon Nov 28 08:20:19 2022 +0000
[
@@ -8,16 +8,18 @@
     <expand macro="version_command"/>
     <command detect_errors="exit_code">
     <![CDATA[
+ln -s '$input_file' input.gfa &&
+
 @HEADLESS@
 Bandage
     info
-    '$input_file'
+    input.gfa
     $tsv
     | sed 's/:\s\+/:\t/g'
     > out.tab
     ]]></command>
     <inputs>
-        <param name="input_file" type="data" format="txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/>
+        <param name="input_file" type="data" format="gfa1,gfa2,fastg,txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/>
         <param argument="--tsv" type="boolean" checked="false" truevalue="--tsv" falsevalue="" label="Output the information in a single tab-delimited line starting with the graph file"/>
     </inputs>
     <outputs>
@@ -25,22 +27,24 @@
     </outputs>
     <tests>
         <test>
-            <param name="input_file" ftype="tabular" value="gfa.tabular"/>
+            <param name="input_file" ftype="txt" value="bandage_input.txt"/>
             <param name="tsv" value="True"/>
             <output name="outfile" ftype="tabular" file="out.tab" compare="contains"/>
         </test>
         <test>
-            <param name="input_file" ftype="tabular" value="gfa.tabular"/>
+            <param name="input_file" ftype="txt" value="bandage_input.txt"/>
             <output name="outfile" ftype="tabular" file="out_standard.tab"/>
         </test>
     </tests>
     <help><![CDATA[
 
+*THE NEW BANDAGE: As of version 2022.09, the Bandage tool is now built on `Bandage-NG <https://github.com/asl/BandageNG>`_. This fork of the original Bandage is better maintained with additional features and performance upgrades.*
+
 @BANDAGE_OVERVIEW@
 
 **Command Documentation**
 
-``Bandage info`` takes a graph file as input and outputs the following statistics about the graph:
+``Bandage info`` takes a graph file (GFA) as input and outputs the following statistics about the graph:
 
 - **Node count:** The number of nodes in the graph. Only positive nodes are counted (i.e. each complementary pair counts as one).
 - **Edge count:** The number of edges in the graph. Only one edge in each complementary pair is counted.
b
diff -r 21e491ad532a -r ddddce450736 macros.xml
--- a/macros.xml Tue Nov 01 15:09:04 2022 +0000
+++ b/macros.xml Mon Nov 28 08:20:19 2022 +0000
b
@@ -1,8 +1,8 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.8.1</token>
+    <token name="@TOOL_VERSION@">2022.09</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@TOOL_VERSION@">bandage</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">bandage_ng</requirement>
         </requirements>
     </xml>
     <xml name="version_command">
b
diff -r 21e491ad532a -r ddddce450736 test-data/gfa.tabular
--- a/test-data/gfa.tabular Tue Nov 01 15:09:04 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,3540 +0,0 @@\n-S\tutg000001l\tGAAATCATCAGGCGTTTTTCACGATATGGACGGGAAGATGCGGAAATAGGCAGGAGGACATAGAAATGCCTGAGGGGTCTGGGATGGTGCGGGCAACGGATGTTATGGTAAATAAGCTTCCGTTGGTAAACCTGTAAGTTTTCAGGAACGAGACTCGTTTAGAACATCTAAAAAGCACATGAATGCTGCTATAGAAGCGACTGTTTGATGGTTCATGGTTTTATATTAAGGTAGATGAAAACTCAATACAGCGCTATTTAGAGACGCTTAAATGGCATTCTTGTATTTTAACGATGCAGAGTAACAGGCTCTAGCTAGTTATAGTACATCGAAAAGTTCATATAGGGACAAAACAAAGGGACTGAAATACATAGCCATAAGCTCGCTTCAAAGTCCTAACCACCAGCTATATTGCATGGGTTTGGTTAAGACATACGTCATGTCTTTGGGGCATATTATGGTGAAAAACGCGTTCATCTACACCAATATTTATACATTTCTCTTCAATAATGACGCCGTTTCCAGCCAACTTTGCTATATGGGTGACAATTTTCGCTTTTAAACGGAGATGTCTCCATGATTGAGCAGATCTAAAAATCTGCATTTTGTGCTGTGCAGGCATTACCATTCTTTCTATGCACAAACGTGCCGCGTCTTGCATTCTGCTTTGTATGCGGAGGTGCTCAATGAGGCTTTAACTACTCCCCTCCGTTAACGCCGTTCGTGTTTTAAACCGCCTTCTCGATAAAGAGTTTCACAGGTGCTGAAGAAATTCGCCTTTACGATGATCAGGGCGGGTGATTGGTACATCAACAACAGGCTTCTTGTTCTGTTTTGAGAGCATGAAGATCAGCCGCGATGGTAATATGTTCGTGTATTTGTCTCAAATACATTGATGACTATTACAACCGTCGTGAGTATCAGTTTAGTCAGCAGAGGCATGCTGTCGCTGTGCTCGTCAGCATAGAAAAGCCTCTACGGCCGCTCGTTTGCTTTTATCGCTAGGTGAGCTTGTCCCAGAAAGTATCCGTATGATTCTTGCGCTAATGATGATTAGGGGATATTATGTTTCTGGGGTTATTTTGTTGTTTTGCTGGCTTTCTCTACTATTAGAGAGCTTGGGGTTTCTTGGAAACGTTGAATGGGGTCCTCTAGCATGATTTGTTTGAGCTTCATCTGGTCTATGAAGCAGTCAGGAAGAGTCTTAAGCACGATGTTGGGTCTTAAACTAGACTAAAAATATAATATGCGAGCTTTTAACTCATAGACGTGTAGTTTTCACTCTTTTTGCTGGTGTTCTAAGCAAAAACTTCTGCATTACGCCTGTTTGTGGTTGCCTGTTATAAGATAACAGTAAAATCCATGCGTTTCTAAGGAGAAAATGAACAAAAGCTATCACTAAATCGTATTTCCAATAGAGGTTTCGTCCTCTTTGAAAGGGGTAGTTCATGAAAATTAGTTCATGGAAATGTTTATGATTTAGGTTGGAGTTATTAGGCGCAAAGAAGAAATATAAAAGGATAATTGAAGTTCTAAATCATTATGGTGATTGAGAGGCGTTATGAGCACAGCTAAGGAAAGTTAAGGAAAAAGGCACTCCAATGAGTAGTGCCAATGAATATTCTGGTCGTGATAGTATGAATCAAGATTACATCTAGGCAATCCATGGATATTATTATAGGTTTCTGTGGGCTGTTGGTTCGGTATTAAGTCAATTGTAGATGTAACCGAAGAAGAACTGAAGATTTAGGATACGAAGTATATAGGATAAGAGTTAGCGATCTTATCAGAAACTTTTTCTGAGTGGTGGGGATACATCTACTCCATTCAAAAGATATAATTCCTTGCGGGATTTTGGTGATTCCTTAAGATGTAGAGTACTACCCACACATACTAGCTGAAGCTGTAATTCATGAAATAAAGATAGAAAAATCTAGAAGGAAAATCAAAGGTTAAAGAAACGACTTTCCTTATGAATCAACTAAAAACATAAGATGAAGTGAGTTGCCCAAGTGGTCTAACATAATTTCTATTTATTAGGTGATAGGGCGAAACTGAAAGAAAAGAAATCTTCGAGATAGGGGTTTAAGCAAATCTGAAGTTGATATAATCATCCATCATGACAGGAGTCTGAGCACCCTTATGGCCAGCAAACAGCAAAAGCTATACTTGATGCTGACTATTTTGTTAAAATAATCAGGCCAGAGCTCACCTTAAATCTAAGTTAAACGCTTTCTTGGTCTATTCATGGGCTTAATGGCCTTACGCCAAACGCGCATGAGGAAGACATGTACGCAGCTCATTCTGCCTCTTTACAATCTGCATGTCTTTCCAGACAGGTAGGTGCTGCTATTTTAGATATAAAGGAAATTTAATTGCTGTTGGGCGCAATGATGTTCTAAATTTAACAGTGTGGCCTTTATAGTGCTGATGATGGTGAATGATCATCGCTGTGTCTACAAAGGTGGCAAATGTTACAATGAAGCAAGAAAATTAAATAAAGATAAATACAGCAAATATTGCTTTTCTGATAGGTTAAGAATTTGTCTGTTCAGTTAACTCAAGAACAAGCAGAAAAGGTTGCTGGAATGTCTACGAAGGTACTCCTGTATCATCAATCGACAGTACTCGCTCTATTCATGCTGAAATGGATGCTTCACAGCCCATCTTGCTAGACTCGAGATAGTGGTTTTGAAGATAAGGTTTTATATACAACTACGTTCCCCTGTCATAATTGTGCAGGGTATATTGTTGCTGTTGGTATCAATAAAGTTGTTTATTGAACATATGAAAAAGCAGCTTTAGAGTTGCTGATGATGCAATAACTAGAAGTTAACGAAAGTGGTAAAGTTTTATTTGAGTCCTTTGAAGGGGTTTCTACTGGAATATCATAGAAGTTCTTCTTTTCTACAGATGAAAGGATAGTAAGGTAATGCGGAGAAATATTCAACGAAGTATAAGAATCATATTGATATACAGTTTATTGATAGTTGGATTTTAATCGTGTGGCGGATATTTTCATTAACACAAAACAGATGCTGAAGCTCAAGTAGCCGTTCCATCTGGGACATAGTTAATCCGCTTCTGCCACCGATTCTCGACACCACCAACATCGGGTATGAATCTGTGACTCTGATGTTACAGAGCTTAATCTTGTGTACCAAAAACCACCATACCAACGGTGGTTTTCTCTGAGCTACTGCTCTTTGAGCCGAGGTAACTGGCTTGGAGGAGCTCAGTCACCAAAACTTGTTCTTTCAGTTTAGCCTTAACAGGCGCACAACTTAAGATGCTCCTCTAAATCAGTTACCAGTGGCTGCTGCCAGTGGCGCTTTGTCGTGCCTTCTGGGTTGGACTCAAGACGATAGTTACCGGGGCAGGCGCAGCGGTCGGACTGAACGGGGTTCGTGCGCTGGTCAGCTTGGGCGAACTGCCTGCGGAACGCTGAGTGTCAGGCGATGAGTAAAGTTTAAACAGCCATAACAGCAGGTGAAGAGCACCCCGGTGCCAAACCGAAGGCAGGAACAGAGCGCAGGGAGCTACCGGGGAAACGCAGGATCTTTATAGTCCTGTCCGGGTTTCGCCACCATGATTTGAGCGTCAGATTCTGTGATGCTTGTCAGGGGGCGGAGCCTATCGGAAAACCGGCAACGCGGCCTTTCTTGTTGCTTCTCCCATTCTCTCATTGCCTATGGCTTAATGTCTCTGTTCCCTCCGCTCGCCGCAGCGAACGACCGAGCGGGCGAGTCAGTGAGCGGAAGCGGAATATCTGCGGGCTTCTCTTTGGCACCGTACGCCATAGCGCATTTTAATACGATGCAGAATAGGGCGGGTACGCCGCAAAGTGACGTCACCTGACGTTCTGGATTACAAAGGTTAAAGCAGCGGACAGGAAATGTTTTGTGCCTAGCTATGCTATTCACAAGTAGCAGGACAGATGTGTTTTGGAGTACCATGACATAAAGA'..b'late:97-4044\t+\t20eacfe4-db35-47f6-9c80-de0f37de1966_Basecall_1D_template:97-4044\t-\n-x\tutg000431l\t4428\t1\t2\t2\t17c0b454-e5b5-4eca-8409-8f959c64cbef_Basecall_1D_template:90-4517\t+\t17c0b454-e5b5-4eca-8409-8f959c64cbef_Basecall_1D_template:90-4517\t-\n-x\tutg000432l\t4092\t1\t2\t2\tchannel_131_1b8d5e7f-4d3d-41d1-ad51-1605893bebd9_template:112-4203\t+\tchannel_131_1b8d5e7f-4d3d-41d1-ad51-1605893bebd9_template:112-4203\t-\n-x\tutg000433l\t4186\t1\t2\t2\tchannel_372_6268b812-af3b-4b57-9db1-191548590945_template:103-4288\t+\tchannel_372_6268b812-af3b-4b57-9db1-191548590945_template:103-4288\t-\n-x\tutg000434l\t4191\t1\t2\t3\tchannel_6_a1d0c8d3-50f0-4fd7-b2f7-9018177a4155_template:114-4304\t+\tchannel_6_a1d0c8d3-50f0-4fd7-b2f7-9018177a4155_template:114-4304\t-\n-x\tutg000435l\t3938\t1\t1\t3\t1f2cd90d-b534-4a1c-ba6f-604673eb4575_Basecall_1D_template:151-4088\t+\t1f2cd90d-b534-4a1c-ba6f-604673eb4575_Basecall_1D_template:151-4088\t-\n-x\tutg000436l\t4504\t1\t5\t5\t13ffeb64-1872-4808-b918-00379a10d84e_Basecall_1D_template:114-4617\t+\t13ffeb64-1872-4808-b918-00379a10d84e_Basecall_1D_template:114-4617\t-\n-x\tutg000437l\t4426\t1\t2\t2\t14dd9f09-6471-483f-9dbc-5eeab2d05b9b_Basecall_1D_template:122-4547\t+\t14dd9f09-6471-483f-9dbc-5eeab2d05b9b_Basecall_1D_template:122-4547\t-\n-x\tutg000438l\t4378\t1\t3\t1\t3e84fe1f-6ebd-4d9e-83df-4935355d7a1b_Basecall_1D_template:112-4489\t+\t3e84fe1f-6ebd-4d9e-83df-4935355d7a1b_Basecall_1D_template:112-4489\t-\n-x\tutg000439l\t4419\t1\t2\t3\t1ddfc7e9-6da2-45ba-a9f6-a402db77f48f_Basecall_1D_template:90-4508\t+\t1ddfc7e9-6da2-45ba-a9f6-a402db77f48f_Basecall_1D_template:90-4508\t-\n-x\tutg000440l\t4465\t1\t4\t2\t236014b3-d885-43ad-b2f6-0214e8bada0b_Basecall_1D_template:105-4569\t+\t236014b3-d885-43ad-b2f6-0214e8bada0b_Basecall_1D_template:105-4569\t-\n-x\tutg000441l\t4439\t1\t3\t3\t4227ba5c-a96e-496f-bff4-f7960d9859f3_Basecall_1D_template:95-4533\t+\t4227ba5c-a96e-496f-bff4-f7960d9859f3_Basecall_1D_template:95-4533\t-\n-x\tutg000442l\t4439\t1\t2\t1\t25693aa2-467e-4b02-a3bd-246fe85dfa82_Basecall_1D_template:110-4548\t+\t25693aa2-467e-4b02-a3bd-246fe85dfa82_Basecall_1D_template:110-4548\t-\n-x\tutg000443l\t4269\t1\t1\t1\t5e94309f-ed4e-4c82-a255-1f20604f3cdb_Basecall_1D_template:108-4376\t+\t5e94309f-ed4e-4c82-a255-1f20604f3cdb_Basecall_1D_template:108-4376\t-\n-x\tutg000444l\t4346\t1\t2\t1\t112f5d59-11ee-4990-b07d-c036bc4a6d31_Basecall_1D_template:105-4450\t+\t112f5d59-11ee-4990-b07d-c036bc4a6d31_Basecall_1D_template:105-4450\t-\n-x\tutg000445l\t4153\t1\t3\t2\tchannel_93_02194193-3ab2-4f66-829b-84853323c30b_template:99-4251\t+\tchannel_93_02194193-3ab2-4f66-829b-84853323c30b_template:99-4251\t-\n-x\tutg000446l\t4462\t1\t1\t4\t1a033013-d2e8-4de9-b658-3476a51d913d_Basecall_1D_template:113-4574\t+\t1a033013-d2e8-4de9-b658-3476a51d913d_Basecall_1D_template:113-4574\t-\n-x\tutg000447l\t4356\t1\t2\t2\t0c50deb8-0c6e-40c5-a634-4e7f154df450_Basecall_1D_template:103-4458\t+\t0c50deb8-0c6e-40c5-a634-4e7f154df450_Basecall_1D_template:103-4458\t-\n-x\tutg000448l\t1889\t5\t0\t0\tchannel_281_ded88d6b-c329-4db2-a443-bd2cdc95f79b_template:126-1699\t-\tchannel_278_9f150893-71db-4f68-b680-c8b06fc6661a_template:113-1811\t-\n-x\tutg000449l\t4290\t1\t1\t2\t043a6ff7-d5db-4f63-97c0-9bc40b1c15da_Basecall_1D_template:93-4382\t+\t043a6ff7-d5db-4f63-97c0-9bc40b1c15da_Basecall_1D_template:93-4382\t-\n-x\tutg000450l\t4503\t1\t2\t5\t04be1f10-9be5-4ff4-8d3f-b90030d7cc06_Basecall_1D_template:107-4609\t+\t04be1f10-9be5-4ff4-8d3f-b90030d7cc06_Basecall_1D_template:107-4609\t-\n-x\tutg000451l\t4495\t1\t2\t3\t04b60356-87f8-4e60-b31a-c1a1afd81db9_Basecall_1D_template:120-4614\t+\t04b60356-87f8-4e60-b31a-c1a1afd81db9_Basecall_1D_template:120-4614\t-\n-x\tutg000452l\t4209\t1\t2\t1\t8044f3f5-5dbd-4d83-af0b-9deccec3c16d_Basecall_1D_template:107-4315\t+\t8044f3f5-5dbd-4d83-af0b-9deccec3c16d_Basecall_1D_template:107-4315\t-\n-x\tutg000453l\t4477\t1\t1\t3\t061fd347-ea8c-4c10-b5cf-18c9a3b544e3_Basecall_1D_template:105-4581\t+\t061fd347-ea8c-4c10-b5cf-18c9a3b544e3_Basecall_1D_template:105-4581\t-\n-x\tutg000454c\t736\t2\n-x\tutg000455l\t4449\t1\t2\t3\t006d5fde-2479-4715-801e-dc83e2c72ece_Basecall_1D_template:121-4569\t+\t006d5fde-2479-4715-801e-dc83e2c72ece_Basecall_1D_template:121-4569\t-\n'
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diff -r 21e491ad532a -r ddddce450736 test-data/out.jpg
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Binary file test-data/out.jpg has changed
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diff -r 21e491ad532a -r ddddce450736 test-data/out.png
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Binary file test-data/out.png has changed
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diff -r 21e491ad532a -r ddddce450736 test-data/out.svg
--- a/test-data/out.svg Tue Nov 01 15:09:04 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 21e491ad532a -r ddddce450736 test-data/out.tab
--- a/test-data/out.tab Tue Nov 01 15:09:04 2022 +0000
+++ b/test-data/out.tab Mon Nov 28 08:20:19 2022 +0000
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diff -r 21e491ad532a -r ddddce450736 test-data/out_fontsize.jpg
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Binary file test-data/out_fontsize.jpg has changed
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diff -r 21e491ad532a -r ddddce450736 test-data/out_labels.svg
--- a/test-data/out_labels.svg Tue Nov 01 15:09:04 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 21e491ad532a -r ddddce450736 test-data/out_standard.tab
--- a/test-data/out_standard.tab Tue Nov 01 15:09:04 2022 +0000
+++ b/test-data/out_standard.tab Mon Nov 28 08:20:19 2022 +0000
b
@@ -1,19 +1,19 @@
-Node count: 455
-Edge count: 1061
-Smallest edge overlap (bp): 3348
-Largest edge overlap (bp): 4532
-Total length (bp): 2238438
-Total length no overlaps (bp): 268863
-Dead ends: 12
-Percentage dead ends: 1.31868%
-Connected components: 7
-Largest component (bp): 1960789
-Total length orphaned nodes (bp): 1960789
-N50 (bp): 4421
-Shortest node (bp): 736
-Lower quartile node (bp): 4290
-Median node (bp): 4404
-Upper quartile node (bp): 4460
-Longest node (bp): 147170
-Median depth: 1
-Estimated sequence length (bp): 297647
+Node count: 3
+Edge count: 4
+Smallest edge overlap (bp): 0
+Largest edge overlap (bp): 0
+Total length (bp): 116705
+Total length no overlaps (bp): 116705
+Dead ends: 0
+Percentage dead ends: 0%
+Connected components: 1
+Largest component (bp): 116705
+Total length orphaned nodes (bp): 0
+N50 (bp): 77945
+Shortest node (bp): 10875
+Lower quartile node (bp): 19380
+Median node (bp): 27885
+Upper quartile node (bp): 52915
+Longest node (bp): 77945
+Median depth: 0
+Estimated sequence length (bp): 0