{"action":"created","comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/37741843","id":37741843,"diff_hunk":"@@ -0,0 +1,132 @@\n+<tool id=\"bwtool-lift\" name=\"bwtool-lift\" version=\"1.0\">\n+    <description>Project data base-by-base into a new assembly using a liftOver chain file from UCSC</description>\n+    <requirements>\n+        <requirement type=\"package\" version=\"1.0\">bwtool</requirement>\n+    </requirements>\n+    <stdio>\n+        <exit_code range=\"1:\" />\n+        <exit_code range=\":-1\" />\n+        <regex match=\"Error:\" />\n+        <regex match=\"Exception:\" />\n+    </stdio>\n+    <command>\n+<![CDATA[\n+    bwtool lift\n+        $input\n+        $to_dbkey\n+        $output\n+        #if $unlifted_regions:\n+            -unlifted=$unlifted_regions_output\n+        #end if\n+\n+        -wigtype=$wigtype\n+\n+        #if $regions:\n+            -regions=$regions\n+        #end if\n+        $condense\n+        #if $fillvalue:\n+            -fill=$fillvalue\n+        #end if\n+]]>\n+    </command>\n+    <inputs>\n+        <param name=\"input\" type=\"data\" format=\"bigwig\" label=\"Convert coordinates of\" />\n+        <param name=\"to_dbkey\" type=\"select\" label=\"To\">\n+            <options from_file=\"liftOver.loc\">\n+                <column name=\"name\" index=\"1\"/>\n+                <column name=\"value\" index=\"2\"/>\n+                <column name=\"dbkey\" index=\"0\"/>\n+                <filter type=\"data_meta\" ref=\"input\" key=\"dbkey\" column=\"0\" />\n+            </options>\n+        </param>\n+\n+        <param name=\"wigtype\" type=\"select\" label=\"Output type\">\n+            <option value=\"bg\">bedGraph</option>\n+            <option value=\"fix\">fixed step wig</option>\n+            <option value=\"var\" selected=\"True\">variable step wig</option>\n+        </param>\n+\n+        <param name=\"regions\" type=\"data\" format=\"bed\" optional=\"True\" label=\"Regions to lift\" hel=\"in BED format (-regions)\"/>\n+\n+        <param name=\"condense\" type=\"boolean\" truevalue=\"-condense\" falsevalue=\"\" checked=\"true\"\n+            label=\"Condense the output\"\n+            help=\"Particularly for bedGraphs. (-condense)\" />\n+\n+        <param name=\"fillvalue\" size=\"10\" type=\"text\" label=\"Filling value\" optional=\"True\"\n+            help=\"Some programs allow filling missing parts of the bigWig with a specified value prior to using data. (-fill)\"/>\n+\n+        <param name=\"unlifted_regions\" type=\"boolean\" label=\"Save all the regions from the input that are not lifted\" help=\"(-unlifted)\"/>\n+\n+    </inputs>\n+    <outputs>\n+        <data format=\"bigwig\" name=\"output\">\n+            <change_format>\n+                <when input=\"wigtype\" value=\"bg\" format=\"bedgraph\" />\n+            </change_format>\n+            <actions>\n+                <action type=\"metadata\" name=\"dbkey\">\n+                    <option type=\"from_file\" name=\"liftOver.loc\" column=\"1\" offset=\"0\">\n+                        <filter type=\"param_value\" column=\"0\" value=\"#\" compare=\"startswith\" keep=\"False\"/>\n+                        <filter type=\"param_value\" ref=\"to_dbkey\" column=\"2\"/>\n+                    </option>\n+                </action>\n+            </actions>\n+        </data>\n+        <data format=\"bigwig\" name=\"unlifted_regions_output\" label=\"${tool.name} on ${on_string}: Unlifted regions\">\n+            <filter>unlifted_regions</filter>","path":"tools/bwtool/bwtool.xml","position":77,"original_position":77,"commit_id":"d4eb2b8ed304841d61dcc69a8ac53b71bd8b9b93","original_commit_id":"d4eb2b8ed304841d61dcc69a8ac53b71bd8b9b93","user":{"login":"nsoranzo","id":4924623,"avatar_url":"https://avatars.githubusercontent.com/u/4924623?v=3","gravatar_id":"","url":"https://api.github.com/users/nsoranzo","html_url":"https://github.com/nsoranzo","followers_url":"https://api.github.com/users/nsoranzo/followers","following_url":"https://api.github.com/users/nsoranzo/following{/other_user}","gists_url":"https://api.github.com/users/nsoranzo/gists{/gist_id}","starred_url":"https://api.github.com/users/nsoranzo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nsoranzo/subscriptions","organizations_url":"https://api.github.com/users/nsoranzo/orgs","repos_url":"https://api.github.com/users/nsoranzo/repos","events_url":"https://api.github.com/users/nsoranzo/events{/privacy}","received_events_url":"https://api.github.com/users/nsoranzo/received_events","type":"User","site_admin":false},"body":"Is the format \"bigwig\" also when wigtype is 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