diff bandage_image.xml @ 8:ddddce450736 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 2b3b163bbe36bb648c17c9b0bf808d41d92078c0

--- 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>
-