Mercurial > repos > jjohnson > contig_annotation_tool

diff cat_bins.xml @ 3:18ece3d5bcde draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 3febcc9ba3d3717877c36bf96742209012a13ac4-dirty
author jjohnson
date Tue, 26 Nov 2019 15:42:14 -0500
parents 9a01840eac52
children aaeb63501369
line wrap: on
line diff
--- a/cat_bins.xml	Mon Nov 25 15:09:24 2019 -0500
+++ b/cat_bins.xml	Tue Nov 26 15:42:14 2019 -0500
@@ -45,10 +45,20 @@
     </outputs>
     <tests>
         <test>
+            <param name="mags" ftype="fasta" value="genome2.fna"/>
+            <expand macro="test_catdb"/>
+            <param name="select_outputs" value="bin2classification"/>
+            <output name="bin2classification">
+                <assert_contents>
+                    <has_text text="666" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
             <param name="mags" ftype="fasta" value="genome3.fna"/>
             <expand macro="test_catdb"/>
-            <param name="select_outputs" value="contig2classification"/>
-            <output name="contig2classification">
+            <param name="select_outputs" value="bin2classification"/>
+            <output name="bin2classification">
                 <assert_contents>
                     <has_text text="1639" />
                 </assert_contents>
@@ -57,14 +67,42 @@
         <test>
             <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
             <expand macro="test_catdb"/>
-            <param name="select_outputs" value="contig2classification"/>
-            <output name="contig2classification">
+            <param name="select_outputs" value="bin2classification"/>
+            <output name="bin2classification">
                 <assert_contents>
                     <has_text text="666" />
                     <has_text text="1639" />
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
+            <expand macro="test_catdb"/>
+            <param name="select_outputs" value="bin2classification"/>
+           <param name="select_outputs" value="predicted_proteins_faa"/>
+            <conditional name="names">
+                <param name="add_names" value="both"/>
+            </conditional>
+            <param name="summarise" value="classification"/>
+            <output name="predicted_proteins_faa">
+                <assert_contents>
+                    <has_text text="contig_11394" />
+                    <has_text text="contig_4403" />
+                </assert_contents>
+            </output>
+            <output name="orf2lca_names">
+                <assert_contents>
+                    <has_text text="Listeria" />
+                    <has_text text="Vibrio" />
+                </assert_contents>
+            </output>
+            <output name="classification_summary">
+                <assert_contents>
+                    <has_text text="Listeria" />
+                </assert_contents>
+            </output>
+        </test>
+
     </tests>
     <help><![CDATA[
 **CAT bin or bins**