diff spyboat.xml @ 1:639d2031d998 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
author iuc
date Mon, 30 Nov 2020 21:11:23 +0000
parents 76733d05d8ef
children 4626a83601d4
line wrap: on
line diff
--- a/spyboat.xml	Sat Nov 28 13:45:34 2020 +0000
+++ b/spyboat.xml	Mon Nov 30 21:11:23 2020 +0000
@@ -1,5 +1,5 @@
-<tool id="spyboat" name="SpyBOAT" version="@TOOL_VERSION@" profile="20.01" license="GPL-3.0-or-later">
-<description>wavelet transforms image stacks</description>
+<tool id="spyboat" name="SpyBOAT" version="@TOOL_VERSION@" profile="20.01"  license="GPL-3.0-or-later">
+<description>wavelet analyzes image stacks</description>
     <macros>
         <token name="@TOOL_VERSION@">0.1.1</token>
     </macros>
@@ -75,21 +75,21 @@
         argparse parser in spyboat_cli.py
         -->
         <section name="PreProc" title="Preprocessing" expanded="true">
-          <param argument="gauss_sigma" type="float" min="0" max="9999999" optional="true" label="Sigma"
+          <param argument="gauss_sigma" type="float" min="0" max="100" optional="true" label="Sigma"
                help="Width of the Gaussian smoothing kernel, leave blank if no pre-smoothing desired" />
           <param argument="rescale_factor" type="integer" value="" min="0" max="99" optional="true" label="Rescale factor"
                help="Downsamples the input movie by this factor given in %, leave blank to disable downsampling" />
         </section>
         <section name="wavana" title="Wavelet Analysis" expanded="true">
-            <param name="dt" type="float" value="1" min="0" max="9999999" label="Sampling interval" help="Time span between two frames" />
-            <param name="tmin" type="float" value="20" min="0" max="9999999" label="Smallest period" help="Lowest period for the wavelet transform" />
-            <param name="tmax" type="float" value="30" min="0" max="9999999" label="Largest period"
+            <param name="dt" type="float" value="1" min="0" max="1000" label="Sampling interval" help="Time span between two frames" />
+            <param name="tmin" type="float" value="20" min="0" max="2000" label="Smallest period" help="Lowest period for the wavelet transform" />
+            <param name="tmax" type="float" value="30" min="0" max="10000" label="Largest period"
                 help="Largest period for the wavelet transform" />
-            <param name="nt" type="integer" value="150" min="0" max="9999999" label="Number of periods to scan for"
+            <param name="nt" type="integer" value="150" min="0" max="1000" label="Number of periods to scan for"
                 help="Determines period resolution of the Wavelet power spectra" />
-            <param name="tcutoff" type="float" value="40" min="0" max="9999999" label="T cutoff"
+            <param name="tcutoff" type="float" value="40" min="0" max="10000" label="T cutoff"
                 help="Cut-off-period for sinc filter detrending, a blank field disables detrending" optional="true" />
-            <param name="win_size" type="float" value="" min="0" max="9999999" optional="true" label="Sliding window size"
+            <param name="win_size" type="float" value="" min="0" max="10000" optional="true" label="Sliding window size"
                 help="Window size for amplitude envelope estimation, leave blank to disable normalization" />
         </section>
         <conditional name="masking">
@@ -100,17 +100,17 @@
             </param>
             <when value="no_masking" />
             <when value="create_static_mask">
-                <param name="mask_frame" type="integer" value="1" min="1" max="99999" label="Create mask from frame"
+                <param name="mask_frame" type="integer" value="1" min="1" max="5000" label="Create mask from frame"
                        help="Creates a static mask from the chosen frame of the input movie." />
-                <param name="mask_thresh" type="float" value="0" min="0" max="999999" label="Threshold"
+                <param name="mask_thresh" type="float" value="0" min="0" max="65000" label="Threshold"
                        help="All pixels below this threshold will be masked in the output." />
             </when>
             <when value="create_dynamic_mask">
-                <param name="mask_thresh" type="float" value="0" min="0" max="999999" label="Threshold"
+                <param name="mask_thresh" type="float" value="0" min="0" max="65000" label="Threshold"
                        help="For each frame of the input, all pixels below this threshold will be masked in the output." />
             </when>
         </conditional>
-        <param name="outputs" type="select" optional="true" multiple="true" label="Select optional outputs" help="">
+        <param name="outputs" type="select" optional="true" multiple="true" label="Select optional outputs" help="" display="checkboxes">
             <option value="save_phase">Phase Movie</option>
             <option value="save_period">Period Movie</option>
             <option value="save_amplitude">Amplitude Movie</option>
@@ -121,19 +121,19 @@
 
     <outputs>
         <data name="phase_out" format="tiff" label="${movie.name[:-4]}_phase">
-            <filter>'save_phase' in ouputs</filter>
+            <filter>outputs and 'save_phase' in outputs</filter>
         </data>
         <data name="period_out" format="tiff" label="${movie.name[:-4]}_period">
-            <filter>'save_period' in outputs</filter>
+            <filter>outputs and 'save_period' in outputs</filter>
         </data>
         <data name="power_out" format="tiff" label="${movie.name[:-4]}_power">
-            <filter>'save_power' in outputs</filter>
+            <filter>outputs and "save_power" in outputs</filter>
         </data>
         <data name="amplitude_out" format="tiff" label="${movie.name[:-4]}_amplitude">
-            <filter>'save_amplitude' in outputs</filter>
+            <filter>outputs and 'save_amplitude' in outputs</filter>
         </data>
         <data name="preprocessed_out" format="tiff" label="${movie.name[:-4]}_preproc">
-            <filter>'save_preprocessed' in outputs</filter>
+            <filter>outputs and 'save_preprocessed' in outputs</filter>
         </data>
         <data name="html_out" format="html" label="Report ${movie.name[:-4]}" />
     </outputs>
@@ -168,7 +168,6 @@
                     <has_size value="1764430" delta="100" />
                 </assert_contents>
             </output>
-            <output name="html_out" file="output1.html" ftype="html"/>
         </test>
         <test expect_num_outputs="4">
             <section name="wavana">
@@ -186,7 +185,6 @@
                     <has_size value="1764430" delta="100" />
                 </assert_contents>
             </output>
-            <output name="html_out" file="output1.html" ftype="html"/>
         </test>
     </tests>
     <help><![CDATA[