Merge pull request #6339 from martenson/ucsc_netfilter

add ucsc netfilter tool

tools/ucsc_tools/ucsc_netfilter/.shed.yml

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+name: ucsc_netfilter
+owner: iuc
+description: Filter out parts of net
+long_description: Part of a UCSC/kent tool set. Note a net is a recursive data structure -- if a parent fails to pass the filter, the children are not even considered.
+homepage_url: http://hgdownload.cse.ucsc.edu/admin/exe/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter
+type: unrestricted
+categories:
+- Sequence Analysis

tools/ucsc_tools/ucsc_netfilter/netfilter.xml

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+<tool id="ucsc_netfilter" name="netFilter" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
+    <description>
+        Filter out parts of net
+    </description>
+    <macros>
+        <token name="@TOOL_VERSION@">469</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">ucsc-netfilter</requirement>
+    </requirements>
+    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    netFilter
+        '$in_net'
+        #if str($synteny.syn_filter) == "filtersyn"
+            $synteny.syntype
+            #if str($synteny.minSynScore)
+                -minSynScore=$synteny.minSynScore
+            #end if
+            #if str($synteny.minSynSize)
+                -minSynSize=$synteny.minSynSize
+            #end if
+            #if str($synteny.minSynAli)
+                -minSynAli=$synteny.minSynAli
+            #end if
+        #end if
+        #if str($minGap)
+            -minGap=$minGap
+        #end if
+        > '$out'
+    ]]></command>
+    <inputs>
+        <param name="in_net" format="ucsc.net" type="data" label="net dataset" help="" />
+
+        <conditional name="synteny">
+            <param name="syn_filter" type="select" label="Filter on synteny?">
+                <option value="skipsyn" selected="true">no</option>
+                <option value="filtersyn">yes</option>
+            </param>
+            <when value="skipsyn" />
+            <when value="filtersyn">
+                <param name="syntype" type="select" display="radio" label="Select synteny filter">
+                    <option value="-syn" selected="true">filter on synteny tuned for human/mouse (-syn)</option>
+                    <option value="-chimpSyn">filter on synteny tuned for human/chimp (-chimpSyn)</option>
+                    <option value="-nonsyn">do inverse filtering based on synteny tuned for human/mouse (-nonsyn)</option>
+                </param>
+                <param argument="-minSynScore" type="integer" optional="true" label="Min syntenic block score" help="default 200,000: covers 27,000 bases including 9,000 aligning--a very stringent requirement." />
+                <param argument="-minSynSize" type="integer" min="0" optional="true" label="Min syntenic block size" help="default 20,000" />
+                <param argument="-minSynAli" type="integer" min="0" optional="true" label="Min syntenic alignment size" help="default 10,000" />
+            </when>
+        </conditional>
+
+        <param argument="-minGap" type="integer" min="0" optional="true" label="Minimum gap" help="Restrict to those with gap size (tSize) >= minSize" />
+    </inputs>
+    <outputs>
+        <data name="out" format="ucsc.net" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="in_net" value="in.ucsc.net" />
+            <conditional name="synteny">
+                <param name="syn_filter" value="filtersyn" />
+                <param name="syntype" value="-chimpSyn" />
+            </conditional>
+            <param name="minGap" value="300" />
+            <output name="out" file="out.ucsc.net" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`netFilter`_ is a tool to filter out parts of net. What passes filter goes to output. Note a net is a recursive data structure. If a parent fails to pass the filter, the children are not even considered.
+
+.. _netFilter: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1093/bib/bbs038</citation>
+    </citations>
+</tool>