Add Pairtools sort

tools/pairtools/sort.xml

@@ -0,0 +1,36 @@
+<tool id="pairtools_sort" name="Pairtools sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="22.05" license="MIT">
+    <description>Sort a .pairs/.pairsam file.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        pairtools sort
+            '$pairs_path'
+            -o '$output_sorted_pairs'
+            --nproc-in \${GALAXY_SLOTS:-4}
+            --nproc-out \${GALAXY_SLOTS:-4}
+    ]]></command>
+    <inputs>
+        <param name="pairs_path" type="data" format="text,tabular" label="Input pairs file" help="Input .pairs/.pairsam file"/>
+    </inputs>
+    <outputs>
+        <data name="output_sorted_pairs" format="tabular" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <!--Test default parameters-->
+        <test expect_num_outputs="1">
+            <param name="pairs_path" value="output_parsed_pairs_bam.pairs"/>
+            <output name="output_sorted_pairs" ftype="tabular" file="output_sorted_pairs.pairsam" lines_diff="10"/>
+        </test>
+
+    </tests>
+    <help><![CDATA[
+        **Pairtools sort**
+
+        Sort pairs in the lexicographic order along chrom1 and chrom2, in the numeric order along pos1 and pos2 and in the lexicographic order along pair_type.
+
+    ]]></help>
+    <expand macro="citations"/>
+    <expand macro="creator"/>
+</tool>