--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chainnet.xml	Fri Aug 30 17:53:36 2024 +0000
@@ -0,0 +1,146 @@
+<tool id="ucsc_chainnet" name="chainNet" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
+    <description>
+        make alignment nets out of alignment chains
+    </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-chainnet</requirement>
+    </requirements>
+    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    chainNet
+        '$in_chain'
+        #if str( $target_reference_index_source.target_reference_index_source_selector ) == "history":
+            '${target_reference_index_source.in_tar_ref_index}'
+        #else:
+            '$target_reference_index_source.tar_ref_index_file.fields.path'
+        #end if
+        #if str( $query_reference_index_source.query_reference_index_source_selector ) == "history":
+            '${query_reference_index_source.in_que_ref_index}'
+        #else:
+            '$query_reference_index_source.que_ref_index_file.fields.path'
+        #end if
+        '$targetNet'
+        '$queryNet'
+        #if str($minSpace)
+            -minSpace=$minSpace
+        #end if
+        #if str($minFill)
+            -minFill=$minFill
+        #end if
+        #if str($minScore)
+            -minScore=$minScore
+        #end if
+        $inclHap
+        #if str($verbose)
+            -verbose=$verbose
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="in_chain" format="chain" type="data" label="Chain dataset" help="Select chain dataset" />
+
+        <conditional name="target_reference_index_source">
+            <param name="target_reference_index_source_selector" type="select" label="Choose the source for the target reference genome index">
+                <option value="cached">Built-in</option>
+                <option value="history">From history</option>
+            </param>
+            <when value="cached">
+                <param name="tar_ref_index_file" type="select" label="Using reference genome index">
+                  <options from_data_table="fasta_indexes" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="in_tar_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for target sequence. Typically a '.fai' file." />
+            </when>
+        </conditional>
+
+        <conditional name="query_reference_index_source">
+            <param name="query_reference_index_source_selector" type="select" label="Choose the source for the query reference genome index">
+                <option value="cached">Built-in</option>
+                <option value="history">From history</option>
+            </param>
+            <when value="cached">
+                <param name="que_ref_index_file" type="select" label="Using reference genome index">
+                  <options from_data_table="fasta_indexes" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="in_que_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for query sequence. Typically a '.fai' file." />
+            </when>
+        </conditional>
+
+        <param argument="-minSpace" type="integer" optional="true" min="0" label="Minimum gap size to fill" help="default 25" />
+        <param argument="-minFill" type="integer" optional="true" min="0" label="Minimum fill to record" help="default half of minSpace" />
+        <param argument="-minScore" type="integer" optional="true" label="Minimum chain score to consider" help="default 2000" />
+        <param argument="-inclHap" type="boolean" optional="true" truevalue="-inclHap" falsevalue="" label="Include query sequences name in the form *_hap*|*_alt*. Normally these are excluded from nets as being haplotype pseudochromosomes." />
+        <param argument="-verbose" type="integer" optional="true" label="Verbosity" help="default 1" />
+
+    </inputs>
+    <outputs>
+        <data name="targetNet" format="ucsc.net" label="${tool.name} on ${on_string}: target.net"/>
+        <data name="queryNet" format="ucsc.net" label="${tool.name} on ${on_string}: query.net" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="in_chain" value="input.chain" />
+            <conditional name="target_reference_index_source">
+                <param name="target_reference_index_source_selector" value="history" />
+                <param name="in_tar_ref_index" value="hg38.chr20.chunk.fasta.fai"/>
+            </conditional>
+            <conditional name="query_reference_index_source">
+                <param name="query_reference_index_source_selector" value="history" />
+                <param name="in_que_ref_index" value="mm39.chr2.chunk.fasta.fai"/>
+            </conditional>
+            <output name="targetNet" file="target.net"/>
+            <output name="queryNet" file="query.net"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="in_chain" value="input.chain" />
+            <conditional name="target_reference_index_source">
+                <param name="target_reference_index_source_selector" value="cached" />
+                <param name="tar_ref_index_file" value="hg38.chr20.chunk"/>
+            </conditional>
+            <conditional name="query_reference_index_source">
+                <param name="query_reference_index_source_selector" value="cached" />
+                <param name="que_ref_index_file" value="mm39.chr2.chunk"/>
+            </conditional>
+            <output name="targetNet" file="target.net"/>
+            <output name="queryNet" file="query.net"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="in_chain" value="input.chain" />
+            <param name="minScore" value="1200" />
+            <conditional name="target_reference_index_source">
+                <param name="target_reference_index_source_selector" value="cached" />
+                <param name="tar_ref_index_file" value="hg38.chr20.chunk"/>
+            </conditional>
+            <conditional name="query_reference_index_source">
+                <param name="query_reference_index_source_selector" value="history" />
+                <param name="in_que_ref_index" value="mm39.chr2.chunk.fasta.fai"/>
+            </conditional>
+            <output name="targetNet" file="target.1200.net"/>
+            <output name="queryNet" file="query.1200.net"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`chainNet`_ is a tool that makes alignment nets out of `alignment chains`_.
+It outputs two files in the `ucsc.net`_ format -- one for the target sequence and one for the query sequence.
+
+For implementation details see ChainNet's `source code`_.
+
+.. _chainNet: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
+.. _ucsc.net: https://genome.ucsc.edu/goldenPath/help/net.html
+.. _alignment chains: https://genome.ucsc.edu/goldenPath/help/chain.html
+.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/chainNet/chainNet.c
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1093/bib/bbs038</citation>
+    </citations>
+</tool>