diff delete_features.xml @ 10:df0e4eb2dfa5 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"

--- a/delete_features.xml	Mon Jul 29 10:09:19 2019 -0400
+++ b/delete_features.xml	Mon Dec 02 05:44:41 2019 -0500
@@ -7,29 +7,32 @@
   <expand macro="requirements"/>
   <code file="webapollo.py"/>
   <command detect_errors="aggressive"><![CDATA[
+@AUTH@
+
 #if str($ask_one) == "yes":
 	## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
-	python $__tool_directory__/export.py
-	@ADMIN_AUTH@
+	python '$__tool_directory__/export.py'
 	@ORG_OR_GUESS@
-	--gff "$gff_out"
-	--fasta "$fasta_out"
-	--json "$json_out"
-    "$__user_email__"
+	--gff '$gff_out'
+        --fasta_pep '$fasta_pep'
+        --fasta_cds '$fasta_cds'
+        --fasta_cdna '$fasta_cdna'
+        --vcf '$vcf_out'
+	--json '$json_out'
+  '$__user_email__'
 
     &&
 
 	## Now we delete
-	python $__tool_directory__/delete_features.py
-	@ADMIN_AUTH@
+	python '$__tool_directory__/delete_features.py'
 	@ORG_OR_GUESS@
-	"$__user_email__"
+	'$__user_email__'
 	#if str($filter) != "all"
 		--type $filter
 	#end if
-	> $output;
+	> '$output';
 #else
-    echo "Nothing to do" > $output;
+    echo "Nothing to do" > '$output';
 #end if
     ]]></command>
   <inputs>
@@ -43,23 +46,49 @@
     <param name="ask_one" type="boolean" truevalue="yes" falsevalue="" label="Are you SURE you want to do this?" help="It will PERMANENTLY delete all of the features on this organism."/>
   </inputs>
   <outputs>
-    <data format="tabular" name="output" label="Process and Error Log">
+    <data format="txt" name="output" label="Process and Error Log">
         <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
     </data>
 
-    <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/>
-    <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/>
-    <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/>
+    <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
+    <data format="fasta" name="fasta_pep" label="Peptide sequences from Apollo"/>
+    <data format="fasta" name="fasta_cds" label="CDS sequences from Apollo"/>
+    <data format="fasta" name="fasta_cdna" label="cDNA sequences from Apollo"/>
+    <data format="vcf" name="vcf_out" label="Sequence alterations from Apollo"/>
+    <data format="json" name="json_out" label="Metadata from Apollo"/>
   </outputs>
   <tests>
-      <test expect_failure="true">
+      <test>
           <conditional name="org_source">
               <param name="source_select" value="direct"/>
-              <param name="org_raw" value="Test org" />
+              <param name="org_raw" value="org4" />
           </conditional>
           <param name="filter" value="all"/>
           <param name="ask_one" value="yes"/>
-          <expand macro="test_result" />
+
+          <output name="gff_out">
+              <assert_contents>
+                  <has_text text="##sequence-region Merlin 1 172788" />
+                  <has_text text="owner=[e-mail];" />
+                  <has_text text="Name=cds-not-under-exon" />
+              </assert_contents>
+          </output>
+          <output name="fasta_pep" file="export/pep.fa" lines_diff="12"/>
+          <output name="fasta_cds" file="export/cds.fa" lines_diff="12"/>
+          <output name="fasta_cdna" file="export/cdna.fa" lines_diff="12"/>
+          <output name="vcf_out" file="export/out.vcf" lines_diff="4"/>
+          <output name="json_out">
+              <assert_contents>
+                  <has_text text="org4" />
+                  <has_text text="apollo_shared_dir/org4" />
+              </assert_contents>
+          </output>
+          <output name="output">
+              <assert_contents>
+                  <has_text text="Deleted" />
+                  <has_text text="[type=mRNA]" />
+              </assert_contents>
+          </output>
       </test>
   </tests>
   <help><![CDATA[