diff snpfreqplot.xml @ 1:e362b3143cde draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1bde09fccd1a5412240ebd5c1f34a45ad73cebe2"

--- a/snpfreqplot.xml	Wed Dec 02 21:23:06 2020 +0000
+++ b/snpfreqplot.xml	Thu Dec 10 13:41:29 2020 +0000
@@ -3,14 +3,13 @@
     <description>Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data</description>
     <macros>
         <token name="@VERSION@">1.0</token>
-        <token name="@GALAXY_VERSION@">0</token>
+        <token name="@GALAXY_VERSION@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="4.0">r-base</requirement>
         <requirement type="package" version="1.0.12">r-pheatmap</requirement>
         <requirement type="package" version="1.3.0">r-tidyverse</requirement>
         <requirement type="package" version="1.36.0">bioconductor-variantannotation</requirement>
-        <requirement type="package" version="">xorg-libxt</requirement>
     </requirements>
     <edam_topics>
         <edam_topic>topic_0797</edam_topic>
@@ -187,7 +186,7 @@
                 <param name="color" value="Spectral" />
                 <param name="output_type" value="png" />
             </section>
-            <output name="outfile" ftype="png" value="heatmap.imageopts.png" compare="sim_size" delta="86000" />
+            <output name="outfile" ftype="png" value="heatmap.imageopts.png" compare="sim_size" delta="100000" />
         </test>
         <test expect_num_outputs="1">
             <!-- SVG, clustering defaults -->
@@ -202,7 +201,7 @@
             </section>
             <output name="outfile" ftype="svg">
                 <assert_contents>
-                    <has_text text="viewBox=&quot;0 0 1156 335&quot;" />
+                    <has_text text="viewBox=&quot;0 0 1156 361&quot;" />
                 </assert_contents>
             </output>
         </test>
@@ -219,7 +218,7 @@
                 <param name="ratio" value="1.2" />
                 <param name="output_type" value="jpeg" />
             </section>
-            <output name="outfile" ftype="jpg" value="heatmap.clustering2.jpeg" compare="sim_size" delta="121000" />
+            <output name="outfile" ftype="jpg" value="heatmap.clustering2.jpeg" compare="sim_size" delta="130000" />
         </test>
         <test expect_num_outputs="1">
             <!-- PDF, vcf test -->
@@ -238,7 +237,7 @@
             </section>
             <output name="outfile" ftype="svg">
                 <assert_contents>
-                    <has_text text="viewBox=&quot;0 0 754 271&quot;" />
+                    <has_text text="viewBox=&quot;0 0 754 292&quot;" />
                 </assert_contents>
             </output>
         </test>
@@ -251,7 +250,7 @@
             </section>
             <output name="outfile" ftype="svg">
                 <assert_contents>
-                    <has_text text="viewBox=&quot;0 0 3101 697&quot;" />
+                    <has_text text="viewBox=&quot;0 0 3101 879&quot;" />
                 </assert_contents>
             </output>
         </test>
@@ -292,6 +291,11 @@
    Such files can be produced with SnpSift Extract Fields and can be useful if
    preprocessing of the lists with standard text processing tools is required.
 
+   .. class:: infomark
+
+   To represent empty EFF fields in the tabular format you can choose between
+   ``.`` and the empty string.
+
 ----
 
 Example output: