Mercurial > repos > iuc > iwtomics_plotwithscale

diff macros.xml @ 1:d5c094a879a3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics commit 69ca0c7a7e444f54b56d111e16432f5d8dddb96d
author iuc
date Wed, 21 Feb 2018 14:16:06 -0500
parents 055cf9df3a0b
children
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--- a/macros.xml	Fri Aug 04 17:50:09 2017 -0400
+++ b/macros.xml	Wed Feb 21 14:16:06 2018 -0500
@@ -43,15 +43,7 @@
     <xml name="citations">
         <citations>
             <citation type="doi">10.1080/10485252.2017.1306627</citation>
-            <citation type="bibtex">
-                @MANUAL{
-                        iwtomics,
-                        author = {Cremona, M.A. and Pini, A. and Chiaromonte, F. and Vantini, S.},
-                        title = {IWTomics: Interval-Wise Testing for Omics Data},
-                        note = {R package version 1.0.0},
-                        year = {2017}
-                }
-            </citation>
+            <citation type="doi">10.1093/bioinformatics/bty090</citation>
         </citations>
     </xml>
 
@@ -64,20 +56,20 @@
         <conditional name="conditionalplottype">
             <!-- plot type -->
             <param name="plottype" type="select" label="Plot type">
-            <option value="boxplot">Pointwise quantile curves (boxplot)</option>
-            <option value="curves">Curves (aligned)</option>
+                <option value="boxplot">Pointwise quantile curves (boxplot)</option>
+                <option value="curves">Curves (aligned)</option>
             </param>
-            <!-- conditional choice: plottype=boxplot -->
             <when value="boxplot">
-            <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
-                <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
-                <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
-                <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
-                <repeat name="probabilities" title="Probabilities">
-                <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
-                </repeat>
-            </section>
+                <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
+                    <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
+                    <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+                    <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
+                    <repeat name="probabilities" title="Probabilities">
+                        <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+                    </repeat>
+                </section>
             </when>
+            <when value="curves" />
         </conditional>
     </xml>
 
@@ -87,17 +79,18 @@
             <conditional name="conditionalgroupby">
                 <!-- group by -->
                 <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
-                <option value="none">No plot</option>
-                <option value="test">Group by test</option>
-                <option value="feature">Group by feature</option>
+                    <option value="none">No plot</option>
+                    <option value="test">Group by test</option>
+                    <option value="feature">Group by feature</option>
                 </param>
+                <when value="none" />
                 <when value="test">
-                <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
-                <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
+                    <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+                    <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
                 </when>
                 <when value="feature">
-                <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
-                <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
+                    <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+                    <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
                 </when>
             </conditional>
         </section>