diff bandage_image.xml @ 0:067592b6b312 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bandage_image.xml	Tue Sep 18 05:41:44 2018 -0400
@@ -0,0 +1,70 @@
+<tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy0">
+    <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[
+Bandage
+    image
+    '$input_file'
+    'out.$output_format'
+    #if $height:
+        --height '$height'
+    #end if
+    #if $width:
+        --width '$width'
+    #end if
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="tabular" label="Graphical Fragment Assembly" />
+        <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 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">
+            <change_format>
+                <when input="output_format" value="png" format="png"/>
+                <when input="output_format" value="svg" format="svg"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="tabular" value="gfa.tabular"/>
+            <output name="outfile" ftype="jpg" file="out.jpg" compare="sim_size" delta="70000"/>
+        </test>
+        <test>
+            <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>
+            <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>
+    </tests>
+    <help><![CDATA[
+@BANDAGE_OVERVIEW@
+
+**Command Documentation**
+
+``Bandage image`` will generate an image file of the graph visualisation.
+
+.. image:: $PATH_TO_IMAGES/bandage_graph.png
+   :alt: example bandage plot
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
+