--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mash_dist.xml	Thu Sep 11 10:22:01 2025 +0000
@@ -0,0 +1,93 @@
+<tool id="mash_dist" name="mash dist" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>Estimate distance between query sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xref"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #set REFERENCE = "reference."+$reference.ext
+        #set QUERY = "query."+$query.ext
+        ln -s '$reference' $REFERENCE &&
+        ln -s '$query' $QUERY &&
+        mash dist
+            #if $table_output:
+                -t
+            #end if
+                -p \${GALAXY_SLOTS:-1}
+            #if $pvalue:
+                -v $pvalue
+            #end if
+            #if $distance:
+                -d $distance
+            #end if
+            $REFERENCE
+            $QUERY
+            > '$output'
+            ]]></command>
+    <inputs>
+        <param name="table_output" type="boolean" truevalue="-t" falsevalue="" checked="true" label="Table output?" help="Will not report p-values, but fields will be blank if they do not meet the p-value threshold"/>
+        <param name="reference" type="data" format="@INTYPES@,msh" label="Reference"/>
+        <param name="query" type="data" format="@INTYPES@,msh" label="Query"/>
+        <param name="pvalue" type="float" argument="-v" value="1.0" min="0" max="1.0" label=" Maximum p-value"/>
+        <param name="distance" type="float" argument="-d" value="1.0" min="0" max="1.0" label="Maximum distance"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tsv" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="table_output" value="true"/>
+            <param name="reference" value="ERR024951_seqtk_sample_1000_1.fastq" ftype="fastqsanger"/>
+            <param name="query" value="ERR024951_seqtk_sample_1000_2.fastq" ftype="fastqsanger"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="0.203604"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+        <param name="table_output" value="true"/>
+        <param name="reference" value="ERR024951_seqtk_sample_1000_1.fastq.gz" ftype="fastqsanger.gz"/>
+        <param name="query" value="ERR024951_seqtk_sample_1000_2.fastq.gz" ftype="fastqsanger.gz"/>
+        <output name="output">
+            <assert_contents>
+                <has_text text="0.203604"/>
+            </assert_contents>
+        </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="table_output" value="true"/>
+            <param name="reference" value="test_06_mash_sketch.msh" ftype="msh"/>
+            <param name="query" value="test_07_mash_sketch.msh" ftype="msh"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="table_output" value="true"/>
+            <param name="reference" value="m64326e_231117_100511.hifi_reads.bc2068--bc2068.msh" ftype="msh"/>
+            <param name="query" value="m64326e_231130_052019.hifi_reads.bc2068--bc2068.msh" ftype="msh"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="0.0149234"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+  Estimate the distance of each query sequence to the reference. Both the
+  reference and queries can be fasta or fastq, gzipped or not, or Mash sketch
+  files (.msh) with matching k-mer sizes. Query files can also be files of file
+  names (see -l). Whole files are compared by default (see -i). The output
+  fields are [reference-ID, query-ID, distance, p-value, shared-hashes].
+
+  ]]></help>
+    <expand macro="citations"/>
+</tool>
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