Mercurial > repos > earlhaminst > ensembl_get_genetree

diff get_genetree.xml @ 4:0602dcf02768 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
author earlhaminst
date Fri, 13 Apr 2018 09:43:28 -0400
parents 181e12d6ac96
children 675fd774314e
line wrap: on
line diff
--- a/get_genetree.xml	Fri Mar 24 11:57:35 2017 -0400
+++ b/get_genetree.xml	Fri Apr 13 09:43:28 2018 -0400
@@ -109,7 +109,26 @@
             <param name="sequence_selector" value="protein" />
             <param name="aligned" value="0" />
             <param name="cigar" value="0" />
-            <output name="output" file="genetree.json" ftype="json" compare="sim_size" />
+            <output name="output" ftype="json">
+                <assert_contents>
+                    <has_text text="tree" />
+                    <has_text text="Euteleostomi" />
+                    <has_text text="ENSG00000139618" />
+                    <has_text text="ENSMUSG00000041147" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_type" value="gene_id" />
+            <param name="input" value="ENSGALP00000027524" />
+            <param name="output_format_selector" value="nh" />
+            <param name="nh_format" value="simple" />
+            <output name="output" ftype="nhx">
+                <assert_contents>
+                    <has_text text="ENSGALP00000027524" />
+                    <has_text text="ENSP00000369497" />
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="input_type" value="gene_tree_id" />
@@ -118,7 +137,14 @@
             <param name="sequence_selector" value="protein" />
             <param name="aligned" value="0" />
             <param name="cigar" value="0" />
-            <output name="output" file="genetree.json" ftype="json" compare="sim_size" />
+            <output name="output" ftype="json">
+                <assert_contents>
+                    <has_text text="tree" />
+                    <has_text text="Euteleostomi" />
+                    <has_text text="ENSG00000139618" />
+                    <has_text text="ENSMUSG00000041147" />
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="input_type" value="gene_tree_id" />
@@ -126,7 +152,14 @@
             <param name="output_format_selector" value="phyloxml" />
             <param name="sequence_selector" value="protein" />
             <param name="aligned" value="0" />
-            <output name="output" file="genetree.phyloxml" ftype="phyloxml" compare="sim_size" />
+            <output name="output" ftype="phyloxml">
+                <assert_contents>
+                    <has_text text="Euteleostomi" />
+                    <has_text text="ENSG00000139618" />
+                    <has_text text="ENSMUSG00000041147" />
+                    <has_text text="&lt;/phyloxml&gt;" />
+                </assert_contents>
+            </output>
         </test>
     </tests>