diff bandage_info.xml @ 8:ddddce450736 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 2b3b163bbe36bb648c17c9b0bf808d41d92078c0
author iuc
date Mon, 28 Nov 2022 08:20:19 +0000
parents b9e31c5c01c7
children
line wrap: on
line diff
--- 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.