Mercurial > repos > iuc > bandage

changeset 5:d8b1027d6ce0 draft

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"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 94fe43e75ddc
children b9e31c5c01c7
files bandage_image.xml bandage_info.xml macros.xml test-data/out.tab test-data/out.txt test-data/out_standard.tab test-data/out_standard.txt
diffstat 7 files changed, 36 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/bandage_image.xml	Tue Jan 19 10:06:26 2021 +0000
+++ b/bandage_image.xml	Sun Sep 12 08:13:13 2021 +0000
@@ -1,5 +1,6 @@
 <tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy3" profile="18.01">
     <description>visualize de novo assembly graphs</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- 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>
-
--- a/macros.xml	Tue Jan 19 10:06:26 2021 +0000
+++ b/macros.xml	Sun Sep 12 08:13:13 2021 +0000
@@ -8,8 +8,12 @@
     <xml name="version_command">
         <version_command>@HEADLESS@ Bandage --version</version_command>
     </xml>
-    <token name="@HEADLESS@"><![CDATA[export QT_QPA_PLATFORM='offscreen' &&]]>
-</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">bandage</xref>
+        </xrefs>
+    </xml>
+    <token name="@HEADLESS@"><![CDATA[export QT_QPA_PLATFORM='offscreen' &&]]></token>
     <token name="@BANDAGE_OVERVIEW@">
 
 **Bandage Overview**
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.tab	Sun Sep 12 08:13:13 2021 +0000
@@ -0,0 +1,2 @@
+455	1061	3348	4532	2238438	268863	12	1.31868%	7	1960789	277649	4421	736	4290	4404	4460	147170	1
+297647
--- a/test-data/out.txt	Tue Jan 19 10:06:26 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-455	1061	3348	4532	2238438	268863	12	1.31868%	7	1960789	277649	4421	736	4290	4404	4460	147170	1
-297647
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_standard.tab	Sun Sep 12 08:13:13 2021 +0000
@@ -0,0 +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
--- a/test-data/out_standard.txt	Tue Jan 19 10:06:26 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-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