--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cooler_cload_tabix.xml	Mon Oct 24 15:19:04 2022 +0000
@@ -0,0 +1,71 @@
+<tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy0" profile="18.01">
+  <description> Create a cool file from a tabix-indexed contact file and a list of genomic bins.</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+  <command detect_errors="exit_code"><![CDATA[
+    ##set up input files
+    ln -s '$input_pairs' pairs.tabix &&
+    #if str( $input_pairs.metadata.tabix_index ) != "None":
+      ln -s '$input_pairs.metadata.tabix_index' pairs.tabix.tbi &&
+    #else:
+      tabix -s $pairs_advanced.c1 -b $pairs_advanced.p1 -e $pairs_advanced.p1 pairs.tabix &&
+    #end if
+    cooler cload tabix --assembly '$assembly' -c2 $c2 -p2 $p2 '$input_bed' pairs.tabix '$output'
+    ]]>
+  </command>
+  <inputs>
+    <param name="input_pairs" multiple="false"  type="data" format="bgzip,tabix" label="Select the output of csort_tabix."/>
+    <section name="pairs_advanced" title="If your input is not already indexed" expanded="False">
+      <param name="c1" type="integer" value="1" label="field number in the input file (starting from 1) of the chromosome of mate 1.">
+        <validator type="in_range" min="1" />
+      </param>
+      <param name="p1" type="integer" value="2" label="field number in the input file (starting from 1) of the position of mate 1.">
+        <validator type="in_range" min="1" />
+      </param>
+    </section>
+    <param name="c2" type="integer" value="3" label="field number in the input file (starting from 1) of the chromosome of mate 2 (same as in csort).">
+      <validator type="in_range" min="1" />
+    </param>
+    <param name="p2" type="integer" value="4" label="field number in the input file (starting from 1) of the position of mate 2 (same as in csort).">
+      <validator type="in_range" min="1" />
+    </param>
+    <param name="assembly" type="text" label="name of genome assembly"/>
+    <param name="input_bed" multiple="false"  type="data" format="bed" label="Select the output of makebins."/>
+  </inputs>
+  
+  <outputs>
+    <data format="cool" name="output" label="cool file from $input_pairs.name and $input_bed.name"/>
+  </outputs>
+  
+  <tests>
+    <!-- For the moment I cannot test this tool -->
+    <!-- <test>
+      <param name="input_pairs" value="input.validPairs.tabix" ftype="bgzip"/>
+      <param name="input_bed" value="chr19.1M.bins"/>
+      <param name="assembly" value="chr19"/>
+      <section name="pairs_advanced">
+        <param name="c1" value="3"/>
+        <param name="p1" value="4"/>
+      </section>
+      <param name="c2" value="7"/>
+      <param name="p2" value="8"/>
+      <output name="output" file="input.cool" compare="sim_size"/>
+    </test> -->
+  </tests> 
+
+  <help>
+    **cooler cload**
+    tool developped by mirnylab
+    see https://github.com/open2c/cooler
+    and https://cooler.readthedocs.io/en/latest/cli.html#cooler-cload-tabix
+        
+    command-line::
+    
+      cooler cload tabix --assembly assembly -c2 c2 -p2 p2 input_bed input_pairs output
+    
+  </help>
+  <expand macro="citation_cooler" />
+</tool>