Mercurial > repos > iuc > transit_resampling

diff macros.xml @ 0:8ccb1b841efb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
author iuc
date Mon, 17 Dec 2018 11:02:16 -0500
parents
children 1d1ca6b30fbb
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Dec 17 11:02:16 2018 -0500
@@ -0,0 +1,53 @@
+<?xml version="1.0"?>
+<macros>
+	<xml name="citations">
+		<citations>
+			<citation type="doi">10.1371/journal.pcbi.1004401</citation>
+			<yield />
+		</citations>
+	</xml>
+	<xml name="requirements">
+		<requirements>
+			<requirement type="package" version="@VERSION@">transit</requirement>
+			<yield />
+		</requirements>
+	</xml>
+	<token name="@VERSION@">2.3.1</token>
+	<xml name="outputs">
+        <yield />
+        <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />
+    </xml>
+    <xml name="replicates">
+        <param name="replicates" type="select" label="How to handle replicates">
+        	<option value="Mean">Mean</option>
+        	<option value="Sum">Sum</option>
+        </param>
+    </xml>
+    <xml name="inputs">
+        <param name="inputs" type="data" format="wig" multiple="true" label="Input .wig files" />
+        <yield />
+        <param name="annotation" type="data" format="gff3" label="Input annotation" />
+    </xml>
+    <xml name="ignore_tas">
+        <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." />
+        <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." />
+    </xml>
+    <xml name="standard_inputs">
+    	<expand macro="inputs" />
+    	<yield />
+    	<expand macro="ignore_tas" />
+    </xml>
+    <token name="@LINK_INPUTS@">
+        <![CDATA[
+            #set $input_files = ','.join(['input_file_%d.wig' % idx for idx, _ in enumerate(str($inputs).split(','))])
+            #for idx, filename in enumerate(str($inputs).split(',')):
+                ln -s '$filename' input_file_${idx}.wig &&
+            #end for
+            ln -s '$annotation' annotation.dat &&
+        ]]>
+    </token>
+    <token name="@STANDARD_OPTIONS@">
+        -iN $nterm
+        -tC $cterm
+    </token>
+</macros>