diff --git a/tools/salmon/alevin.xml b/tools/salmon/alevin.xml
index 67aca07123..fe645f2b02 100644
--- a/tools/salmon/alevin.xml
+++ b/tools/salmon/alevin.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         mkdir ./index
@@ -269,7 +270,13 @@
                 <param name="freqThreshold" value="5"/>
                 <param name="dumpMtx" value="true"/>
             </section>
-            <output name="quants_mat_mtx" file="alevin_mat_01.mtx" ftype="mtx" sort="true"/>
+            <output name="quants_mat_mtx" file="alevin_mat_01.mtx" compare="sim_size" ftype="mtx">
+                <assert_contents>
+                    <has_text text="MatrixMarket" />
+                    <has_n_columns n="5" />
+                    <has_n_lines n="105" />
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="11">
             <conditional name="refTranscriptSource">
@@ -296,7 +303,13 @@
                 <param name="freqThreshold" value="5"/>
                 <param name="dumpMtx" value="true"/>
             </section>
-            <output name="quants_mat_mtx" file="alevin_mat_02.mtx" ftype="mtx" sort="true"/>
+            <output name="quants_mat_mtx" file="alevin_mat_02.mtx" compare="sim_size" ftype="mtx" >
+                <assert_contents>
+                    <has_text text="MatrixMarket" />
+                    <has_n_columns n="5" />
+                    <has_n_lines n="105" />
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="8">
             <conditional name="refTranscriptSource">
@@ -323,7 +336,13 @@
                 <param name="freqThreshold" value="5"/>
                 <param name="dumpMtx" value="true"/>
             </section>
-            <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx" ftype="mtx" sort="true"/>
+            <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx"  compare="sim_size" ftype="mtx">
+                <assert_contents>
+                    <has_text text="MatrixMarket" />
+                    <has_n_columns n="5" />
+                    <has_n_lines n="105" />
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="14">
             <conditional name="refTranscriptSource">
@@ -347,7 +366,13 @@
             <section name="optional">
                 <param name="dumpMtx" value="true"/>
             </section>
-            <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true"/>
+            <output name="quants_mat_mtx" file="alevin_mat.mtx"  compare="sim_size" ftype="mtx">
+                <assert_contents>
+                    <has_text text="MatrixMarket" />
+                    <has_n_columns n="5" />
+                    <has_n_lines n="17" />
+                </assert_contents>
+            </output>
             <output name="salmon_quant_log" ftype="txt">
                 <assert_contents>
                     <has_text text="Index contained 322 targets"/>
@@ -363,7 +388,7 @@
             <output_collection name="umigraphs" type="list" count="14">
                 <element name="AGTGGGATCTTAACCT">
                     <assert_contents>
-                        <has_size value="4017" delta="1000"/>
+                        <has_size value="4661" delta="1000"/>
                     </assert_contents>
                 </element>
             </output_collection>
diff --git a/tools/salmon/macros.xml b/tools/salmon/macros.xml
index 45ca1efcf6..89ca3c6047 100644
--- a/tools/salmon/macros.xml
+++ b/tools/salmon/macros.xml
@@ -1,8 +1,13 @@
 <macros>
     <token name="@TOOL_VERSION@">1.10.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@IDX_VERSION@">q7</token>
     <token name="@PROFILE_VERSION@">20.01</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">salmon</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
@@ -121,9 +126,10 @@
         label="Discard orphan quasi"
         help="Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates.  The default behavior is to consider orphan mappings if no valid paired mappings exist."/>
         <conditional name="validmap">
-            <param name="validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False"
-            label="Validate mappings"
-            help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."/>
+            <param name="validateMappings" type="select" label="Validate mappings" help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification.">
+                <option value="--validateMappings">True</option>
+                <option value="" selected="true">False</option>
+            </param>
             <when value="--validateMappings">
                 <param name="minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
                 label="Min Score Fraction"
diff --git a/tools/salmon/salmonquant.xml b/tools/salmon/salmonquant.xml
index b2c22d9696..1c850ae95a 100644
--- a/tools/salmon/salmonquant.xml
+++ b/tools/salmon/salmonquant.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[
         #if $quant_type.qtype == "reads":
diff --git a/tools/salmon/salmonquantmerge.xml b/tools/salmon/salmonquantmerge.xml
index f47f208a3a..d056e80c1a 100644
--- a/tools/salmon/salmonquantmerge.xml
+++ b/tools/salmon/salmonquantmerge.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @qmerge@