Mercurial > repos > iuc > ncbi_eutils_elink

changeset 5:9b628ed09553 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dd9b889d83f058d2ddb87a4e7709ee3d93dddd69"
author iuc
date Fri, 27 Aug 2021 11:30:43 +0000
parents 5c42fe46188f
children e4f8623b8b9b
files elink.xml test-data/elink.esearchin_id_alllinks.json
diffstat 2 files changed, 14 insertions(+), 46 deletions(-) [+]
line wrap: on
line diff
--- a/elink.xml	Mon Jan 04 11:46:17 2021 +0000
+++ b/elink.xml	Fri Aug 27 11:30:43 2021 +0000
@@ -35,7 +35,7 @@
     </collection>
   </outputs>
   <tests>
-    <test>
+    <test expect_num_outputs="1">
       <param name="cmd_select" value="neighbor"/>
       <param name="db_select_to" value="pubmed"/>
       <param name="db_select_from_link" value="taxonomy"/>
@@ -45,7 +45,7 @@
       <param name="linkname" value="None"/>
       <output name="default" file="pm-tax-neighbor.xml" ftype="xml"/>
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="cmd_select" value="neighbor"/>
       <param name="db_select_to" value="nuccore"/>
       <param name="db_select_from_link" value="gene"/>
@@ -55,7 +55,7 @@
       <param name="linkname" value="gene_nuccore"/>
       <output name="default" file="elink.esearch_in_xmlid_1link.tabular" ftype="tabular"/>
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="cmd_select" value="neighbor"/>
       <param name="db_select_to" value="nuccore"/>
       <param name="db_select_from_link" value="gene"/>
@@ -63,9 +63,15 @@
       <param name="id_json" value="elink.esearchin_id.json"/>
       <param name="output_format" value="json"/>
       <param name="linkname" value="None"/>
-      <output name="default" file="elink.esearchin_id_alllinks.json" ftype="json"/>
+      <output name="default" ftype="json">
+        <assert_contents>
+          <has_text text="gene_nuccore_refseqrna"/>
+          <has_text text="gene_nuccore"/>
+          <has_text text="1899688395"/>
+        </assert_contents>
+      </output>
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="cmd_select" value="neighbor"/>
       <param name="db_select_to" value="nuccore"/>
       <param name="db_select_from_link" value="gene"/>
@@ -75,7 +81,7 @@
       <param name="linkname" value="gene_nuccore_refseqrna"/>
       <output name="default" file="elink.esearchin_id_1link.xml" ftype="xml"/>
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="cmd_select" value="neighbor_history"/>
       <param name="db_select_to" value="gene"/>
       <param name="db_select_from_link" value="nuccore"/>
@@ -85,7 +91,7 @@
       <param name="linkname" value="nuccore_gene"/>
       <output name="default" file="elink.elinkin_1link_hist.json" ftype="json" lines_diff="2"/>
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="cmd_select" value="neighbor_history"/>
       <param name="db_select_to" value="gene"/>
       <param name="db_select_from_link" value="nuccore"/>
@@ -95,7 +101,7 @@
       <param name="linkname" value="nuccore_gene"/>
       <output name="default" file="elink.elinkin_allalllinks_id.xml" ftype="xml" lines_diff="2"/>
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="cmd_select" value="neighbor_score"/>
       <param name="db_select_to" value="gene"/>
       <param name="db_select_from_link" value="nuccore"/>
--- a/test-data/elink.esearchin_id_alllinks.json	Mon Jan 04 11:46:17 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-{
-    "header": {
-        "type": "elink",
-        "version": "0.3"
-    },
-    "linksets": [
-        {
-            "dbfrom": "gene",
-            "ids": [
-                "118502329"
-            ],
-            "linksetdbs": [
-                {
-                    "dbto": "nuccore",
-                    "linkname": "gene_nuccore",
-                    "links": [
-                        "1899688395",
-                        "1896832511"
-                    ]
-                },
-                {
-                    "dbto": "nuccore",
-                    "linkname": "gene_nuccore_pos",
-                    "links": [
-                        "1896832511"
-                    ]
-                },
-                {
-                    "dbto": "nuccore",
-                    "linkname": "gene_nuccore_refseqrna",
-                    "links": [
-                        "1899688395"
-                    ]
-                }
-            ]
-        }
-    ]
-}