diff --git a/lib/galaxy/web/controllers/library_common.py b/lib/galaxy/web/controllers/library_common.py
index 1b23efec016..fd500070ec8 100644
--- a/lib/galaxy/web/controllers/library_common.py
+++ b/lib/galaxy/web/controllers/library_common.py
@@ -911,7 +911,7 @@ class LibraryCommon( BaseController ):
                 dataset_names = []
                 created_ldda_ids = ''
                 for hda_id in hda_ids:
-                    hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( hda_id )
+                    hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( hda_id ) )
                     if hda:
                         ldda = hda.to_library_dataset_dataset_association( target_folder=folder, replace_dataset=replace_dataset )
                         created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( ldda.id ) )
diff --git a/templates/library/common/common.mako b/templates/library/common/common.mako
index b165d4e9ec4..a80174d3e73 100644
--- a/templates/library/common/common.mako
+++ b/templates/library/common/common.mako
@@ -308,7 +308,7 @@
                         %endif
                         %for hda in history.active_datasets:
                             <div class="form-row">
-                                <input name="hda_ids" value="${hda.id}" type="checkbox"/>${hda.hid}: ${hda.name}
+                                <input name="hda_ids" value="${trans.security.encode_id( hda.id )}" type="checkbox"/>${hda.hid}: ${hda.name}
                             </div>
                         %endfor
                         <div class="form-row">
diff --git a/tools/filters/lav_to_bed.xml b/tools/filters/lav_to_bed.xml
index d58b1d72df7..3063024f6f8 100644
--- a/tools/filters/lav_to_bed.xml
+++ b/tools/filters/lav_to_bed.xml
@@ -9,10 +9,10 @@
     <data name="bed_file2" format="bed"/>
   </outputs>
   <tests>
-    <!-- NOTE: this tool generates 2 output files, but our functional tests currently only handle the last one generated -->
     <test>
       <param name="lav_file" value="2.lav" ftype="lav" />
-      <output name="bed_file2" file="lav_to_bed_out2.bed" />
+      <output name="bed_file2" file="lav_to_bed_out_1.bed" />
+      <output name="bed_file2" file="lav_to_bed_out_2.bed" />
     </test>
   </tests>
   <help>
diff --git a/tools/metag_tools/split_paired_reads.xml b/tools/metag_tools/split_paired_reads.xml
index 3e89c3d06e5..6874ac19e52 100644
--- a/tools/metag_tools/split_paired_reads.xml
+++ b/tools/metag_tools/split_paired_reads.xml
@@ -12,8 +12,9 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="split_paired_reads_test1.fastq" ftype="fastqsanger"/>
-            <output name="output1" file="split_paired_reads_test1.out1" ftype="fastqsanger"/>
+            <param name="input" value="3.fastqsanger" ftype="fastqsanger"/>
+            <output name="output1" file="split_paired_reads_out_1.fastqsanger" ftype="fastqsanger"/>
+            <output name="output2" file="split_paired_reads_out_2.fastqsanger" ftype="fastqsanger"/>
         </test>
     </tests>
 <help>
diff --git a/tools/next_gen_conversion/solid2fastq.xml b/tools/next_gen_conversion/solid2fastq.xml
index 06928dba3ec..c6fc262f2ac 100644
--- a/tools/next_gen_conversion/solid2fastq.xml
+++ b/tools/next_gen_conversion/solid2fastq.xml
@@ -42,26 +42,27 @@
   </outputs>
   <tests>
     <test>
-      <param name="input1" value="fr.csf" ftype="csfasta"/>
-      <param name="input2" value="fr.qual" ftype="qualsolid" />
-      <output name="out_file1" file="f.fastq"/>
+      <param name="input1" value="fr.csfasta" ftype="csfasta"/>
+      <param name="input2" value="fr.qualsolid" ftype="qualsolid" />
       <param name="paired" value="no"/>
       <param name="qual" value="0" />
       <param name="trim_first_base" value="No" />
       <param name="trim_name" value="No" />
       <param name="double_encode" value="No"/>
+      <output name="out_file1" file="solid2fastq_out_1.fastq"/>
     </test>
     <test>
-      <param name="input1" value="fr.csf" ftype="csfasta"/>
-      <param name="input2" value="fr.qual" ftype="qualsolid" />
-      <param name="input3" value="rr.csf" ftype="csfasta"/>
-      <param name="input4" value="rr.qual" ftype="qualsolid" />
-      <output name="out_file1" file="fr_file1.fastq"/>
+      <param name="input1" value="fr.csfasta" ftype="csfasta"/>
+      <param name="input2" value="fr.qualsolid" ftype="qualsolid" />
+      <param name="input3" value="rr.csfasta" ftype="csfasta"/>
+      <param name="input4" value="rr.qualsolid" ftype="qualsolid" />
       <param name="paired" value="yes"/>
       <param name="qual" value="0" />
       <param name="trim_first_base" value="No" />
       <param name="trim_name" value="Yes" />
       <param name="double_encode" value="No"/>
+      <output name="out_file1" file="solid2fastq_out_2.fastq"/>
+      <output name="out_file2" file="solid2fastq_out_3.fastq"/>
     </test>
  </tests>
 <help>