Mercurial > repos > iuc > mummer_mummerplot

diff mummerplot.xml @ 5:fe7926c563f8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit d3549bc73d5fdfdded1c3e63485f5eb98c479d52
author iuc
date Sat, 19 Oct 2024 20:56:11 +0000
parents d42f78f9ab9b
children
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--- a/mummerplot.xml	Sat Nov 27 09:53:51 2021 +0000
+++ b/mummerplot.xml	Sat Oct 19 20:56:11 2024 +0000
@@ -49,7 +49,7 @@
                     <option value="yes">YES</option>
                 </param>
                 <when value="yes">
-                    <param name="layout" type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
+                    <param  type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
                 </when>
                 <when value="no" />
             </conditional>
@@ -75,7 +75,7 @@
         <data name="output_png" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" />
     </outputs>
     <tests>
-        <test>
+        <test  expect_num_outputs="5">
             <param name="delta" value="nucmer.txt" ftype="tabular" />
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
@@ -99,16 +99,16 @@
 **Options:**::
 
 
-    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest 
+    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
                    sequence end
 
-    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default 
-                   color by match dir) If the plot is very sparse, edit the .gp script to plot with 
+    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default
+                   color by match dir) If the plot is very sparse, edit the .gp script to plot with
                    'linespoints' instead of 'lines'
 
     -c             Generate a reference coverage plot (default for .tiling)
 
-    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on 
+    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on
                    either sequence, i.e. a one-to-one mapping of reference and query subsequences
 
     --fat          Layout sequences using fattest alignment only