diff bandage_image.xml @ 2:58124285e462 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 87337151f2f9ae1946db8b3a6da1c4f512ae135d
author iuc
date Fri, 05 Jul 2019 11:36:09 -0400
parents ebe4463404b4
children b2860df42e16
line wrap: on
line diff
--- a/bandage_image.xml	Wed May 15 04:11:22 2019 -0400
+++ b/bandage_image.xml	Fri Jul 05 11:36:09 2019 -0400
@@ -1,12 +1,14 @@
-<tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy0">
+<tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy1">
     <description>visualize de novo assembly graphs</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
-    <command detect_errors="exit_code">
-    <![CDATA[
+    <command detect_errors="exit_code"> <![CDATA[
+## set headless mode
+export QT_QPA_PLATFORM='offscreen' &&
+
 Bandage
     image
     '$input_file'
@@ -17,16 +19,21 @@
     #if $width:
         --width '$width'
     #end if
+    $names
+    $lengths
     ]]></command>
     <inputs>
         <param name="input_file" type="data" format="txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/>
         <param argument="--height" type="integer" min="1" value="1000" optional="True" label="Image height" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: 1000."/>
         <param argument="--width" type="integer" min="1" optional="True" label="Image width" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: not set."/>
+        <param argument="--names" type="boolean" truevalue="--names" falsevalue="" label="Node name labels?"/>
+        <param argument="--lengths" type="boolean" truevalue="--lengths" falsevalue="" label="Node length labels?"/>
         <param name="output_format" type="select" label="Produce jpg, png or svg file?">
             <option selected="True" value="jpg">.jpg</option>
             <option value="png">.png</option>
             <option value="svg">.svg</option>
         </param>
+
     </inputs>
     <outputs>
         <data name="outfile" format="jpg" from_work_dir="out.*" label="${tool.name} on ${on_string}: Assembly Graph Image">
@@ -37,22 +44,29 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <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"/>
         </test>
-        <test>
+        <test><!-- test with width and height parameters -->
             <param name="input_file" ftype="tabular" value="gfa.tabular"/>
             <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"/>
         </test>
-        <test>
+        <test><!-- test svg output -->
             <param name="input_file" ftype="tabular" value="gfa.tabular"/>
             <param name="output_format" value="svg"/>
             <output name="outfile" ftype="svg" file="out.svg" compare="sim_size" delta="120000"/>
         </test>
+        <test><!-- test with node name and length labels -->
+            <param name="input_file" ftype="txt" value="gfa.tabular"/>
+            <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"/>
+        </test>
     </tests>
     <help><![CDATA[
 @BANDAGE_OVERVIEW@