Make join1 use proper requirements, move to GALAXY_LIB_TOOLS_VERSIONED

lib/galaxy/tools/__init__.py

@@ -128,7 +128,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "__DATA_FETCH__",
     # Legacy tools bundled with Galaxy.
     "laj_1",
-    "join1",
     "gff2bed1",
     "gff_filter_by_feature_count",
     "aggregate_scores_in_intervals2",
@@ -191,6 +190,7 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "sam_pileup": packaging.version.parse("1.1.3"),
     "vcf_to_maf_customtrack1": packaging.version.parse("1.0.1"),
     "secure_hash_message_digest": packaging.version.parse("0.0.2"),
+    "join1": packaging.version.parse("2.1.3"),
 }
 
 

tools/filters/joiner.xml

@@ -1,15 +1,15 @@
-<tool id="join1" name="Join two Datasets" version="2.1.2">
+<tool id="join1" name="Join two Datasets" version="2.1.3">
   <description>side by side on a specified field</description>
   <requirements>
-    <requirement type="package" version="2.7.13">python</requirement>
+    <requirement type="package" version="19.9.0">galaxy-util</requirement>
   </requirements>
   <command detect_errors="aggressive">
     python '$__tool_directory__/join.py' '$input1' '$input2' $field1 $field2 '$out_file1' $unmatched $partial --index_depth=3 --buffer=50000000 --fill_options_file=$fill_options_file $header
   </command>
   <configfiles>
-    <configfile name="fill_options_file">&lt;%
+    <configfile name="fill_options_file"><![CDATA[<%
 import json
-%&gt;
+%>
 #set $__fill_options = {}
 #if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty':
     #set $__fill_options['fill_unjoined_only'] = $fill_empty_columns['fill_columns_by'].value == 'fill_unjoined_only'
@@ -30,7 +30,7 @@ import json
     #end if
 #end if
 ${json.dumps( __fill_options )}
-    </configfile>
+    ]]></configfile>
   </configfiles>
   <inputs>
     <param format="tabular" name="input1" type="data" label="Join"/>
@@ -174,7 +174,7 @@ ${json.dumps( __fill_options )}
       <output name="out_file1" file="joiner_out7.tab"/>
     </test>
   </tests>
-  <help>
+  <help><![CDATA
 
 .. class:: warningmark
 
@@ -182,7 +182,7 @@ ${json.dumps( __fill_options )}
 
 .. class:: infomark
 
-**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
+**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
 
 -----
 
@@ -221,6 +221,6 @@ Joining the 4th column of Dataset1 with the 1st column of Dataset2, while keepin
   chr1 50 80 geneB geneB Foxp2
   chr5 10 40 geneL
 
-</help>
+]]></help>
 <citations></citations>
 </tool>