diff bandage_info.xml @ 5:d8b1027d6ce0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 7823462e83ff5efbcfd3161f7d471fd07da51611"
author iuc
date Sun, 12 Sep 2021 08:13:13 +0000
parents b2860df42e16
children b9e31c5c01c7
line wrap: on
line diff
--- a/bandage_info.xml	Tue Jan 19 10:06:26 2021 +0000
+++ b/bandage_info.xml	Sun Sep 12 08:13:13 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="bandage_info" name="Bandage Info" version="@TOOL_VERSION@+galaxy1" profile="18.01">
+<tool id="bandage_info" name="Bandage Info" version="@TOOL_VERSION@+galaxy2" profile="18.01">
     <description>determine statistics of de novo assembly graphs</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -12,26 +13,27 @@
     info
     '$input_file'
     $tsv
-    > out.txt
+    | sed 's/:\s\+/:\t/g'
+    > out.tab
     ]]></command>
     <inputs>
         <param name="input_file" type="data" format="txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/>
         <param argument="--tsv" type="boolean" checked="false" truevalue="--tsv" falsevalue="" label="Output the information in a single tab-delimited line starting with the graph file"/>
     </inputs>
     <outputs>
-        <data name="outfile" format="txt" from_work_dir="out.txt" label="${tool.name} on ${on_string}: Assembly Graph Information"/>
+        <data name="outfile" format="tabular" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Assembly Graph Information"/>
     </outputs>
     <tests>
         <test>
             <param name="input_file" ftype="tabular" value="gfa.tabular"/>
             <param name="select_mode" value="info"/>
             <param name="tsv" value="True"/>
-            <output name="outfile" ftype="txt" file="out.txt" compare="contains"/>
+            <output name="outfile" ftype="tabular" file="out.tab" compare="contains"/>
         </test>
         <test>
             <param name="input_file" ftype="tabular" value="gfa.tabular"/>
             <param name="select_mode" value="info"/>
-            <output name="outfile" ftype="txt" file="out_standard.txt"/>
+            <output name="outfile" ftype="tabular" file="out_standard.tab"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -65,7 +67,7 @@
     Percentage dead ends:     2.94118%
     Connected components:     19
     Largest component (bp):   4821329
-    N50 (bp):            90360
+    N50 (bp):                 90360
     Shortest node (bp):       1
     Lower quartile node (bp): 17
     Median node (bp):         87
@@ -75,4 +77,3 @@
     ]]></help>
     <expand macro="citations"/>
 </tool>
-