Mercurial > repos > iuc > ucsc_chainsort

diff chainsort.xml @ 0:7e2d89cef769 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort commit 976ad085a01ae065d02b9f8c9f8788e28d9b85cc
author iuc
date Mon, 26 Aug 2024 13:54:15 +0000
parents
children 754d04fba5b9
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chainsort.xml	Mon Aug 26 13:54:15 2024 +0000
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+<tool id="ucsc_chainsort" name="chainSort" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
+    <description>
+        Sort chains
+    </description>
+    <macros>
+        <token name="@TOOL_VERSION@">455</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">ucsc-chainsort</requirement>
+    </requirements>
+    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    chainSort
+        '$in_chain'
+        $sort_by
+        '$out'
+    ]]></command>
+    <inputs>
+        <param name="in_chain" format="chain" type="data" label="Chain dataset" />
+        <param name="sort_by" type="select" label="Sort">
+            <option value="" selected="true">by score</option>
+            <option value="-target">on target start</option>
+            <option value="-query">on query start</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out" format="chain" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_chain" value="input.chain" />
+            <output name="out" file="sorted_score.chain" />
+        </test>
+        <test>
+            <param name="in_chain" value="input.chain" />
+            <param name="sort_by" value="-query" />
+            <output name="out" file="sorted_query.chain" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`chainSort`_ is a tool to sort chains.
+
+Note this tool loads all chains into memory, so it is not suitable for large datasets. Instead, run chainSort on multiple small dataset, followed by chainMergeSort.
+
+.. _chainSort: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1093/bib/bbs038</citation>
+    </citations>
+</tool>