--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stats.xml	Sun Dec 22 15:40:00 2024 +0000
@@ -0,0 +1,70 @@
+<tool id="pairtools_stats" name="Pairtools Stats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
+    <description>Calculates pairs statistics for input pairs and pairsam files.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        pairtools stats
+            $merge
+            $with_chromsizes
+            $yaml
+            -o '$pairs_output'
+            --nproc-in \${GALAXY_SLOTS:-4}
+            --nproc-out \${GALAXY_SLOTS:-4}
+            #if $input_file:
+                ${str($input_file).replace(',', ' ')}
+            #end if
+    ]]></command>
+    <inputs>
+        <param type="data" name="input_file" format="4dn_pairs,4dn_pairsam" multiple="true" label="Input pairs or pairsam file" help="Input 4dn pairs or pairsam file"></param>
+        <param type="boolean" argument="--merge" truevalue="--merge" falsevalue="" checked="False" label="Merge input stats files" help="If selected, will merge multiple input stats files instead of calculating statistics of .pairs/.pairsam file"></param>
+        <param type="boolean" argument="--with-chromsizes" truevalue="--with-chromsizes" falsevalue="" checked="False" label="Store sizes of chromosomes from the header of the pairs file in the stats file"></param>
+        <param type="boolean" argument="--yaml" truevalue="--yaml" falsevalue="" checked="False" label="Output stats in yaml format instead of table"></param>
+        </inputs>
+    <outputs>
+        <data name="pairs_output" format="tabular" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <!--Test 01 with pair file as input and default parameters-->
+        <test expect_num_outputs="1">
+            <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
+            <param name="merge" value="false"/>
+            <param name="with_chromsizes" value="false"/>
+            <param name="yaml" value="false"/>
+            <output name="pairs_output" ftype="tabular" file="pairs_output.stats"/>
+        </test>
+        <!--Test 02 with multipe input pair files as input and default parameters-->
+        <test expect_num_outputs="1">
+            <param name="input_file" value="pairs_output.stats,pairs_output2.stats"/>
+            <param name="merge" value="true"/>
+            <param name="with_chromsizes" value="false"/>
+            <param name="yaml" value="false"/>
+            <output name="pairs_output" ftype="tabular" file="pairs_output_merged.stats" lines_diff="40"/>
+        </test>
+        <!--Test 03 with pair files as input with additional chromsizes in output-->
+        <test expect_num_outputs="1">
+            <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
+            <param name="merge" value="false"/>
+            <param name="with_chromsizes" value="true"/>
+            <param name="yaml" value="false"/>
+            <output name="pairs_output" ftype="tabular" file="pairs_output_with_chromsize.stats"/>
+        </test>
+         <!--Test 04 with pair files as input and yaml output format-->
+        <test expect_num_outputs="1">
+            <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
+            <param name="merge" value="false"/>
+            <param name="with_chromsizes" value="false"/>
+            <param name="yaml" value="true"/>
+            <output name="pairs_output" ftype="tabular" file="pairs_output_yaml.stats"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    Calculate pairs statistics.
+    
+    By default, uses 4dn pairs or 4dn pairsam file to calculate statistics.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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