Mercurial > repos > iuc > homer_annotatepeaks

diff macros.xml @ 0:adab852c8216 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
author iuc
date Sun, 08 Aug 2021 11:03:29 +0000
parents
children 38d10a69748a
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sun Aug 08 11:03:29 2021 +0000
@@ -0,0 +1,49 @@
+<macros>
+    <token name="@TOOL_VERSION@">4.11</token>
+    <!-- HOMER index version compatible with this version of HOMER
+    This is the HOMER version that introduced the preparsed structure expected
+    by the current version. -->
+    <token name="@IDX_VERSION@">4.11</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">homer</xref>
+        </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="4.11">homer</requirement>
+        </requirements>
+    </xml>
+    <xml name="choose_center">
+        <conditional name="choose_center">
+            <param name="center" type="select" label="Do you want to center your sequence on the peak center?">
+                <option value="centered" selected="True">Yes</option>
+                <option value="manual">No, I want asymetric (raise an error if given was chosen above)</option>
+            </param>
+            <when value="centered"/>
+            <when value="manual">
+                <param name="sizes" type="integer" value="-100" label="sequence start relative to center"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="mask_size">
+        <param argument="-mask" type="boolean" truevalue="True" falsevalue="False" label="mask repeats/lower case sequence"/>
+        <conditional name="fixed_size">
+            <param name="size_fixed" type="select" label="Do you want a fixed fragment size?">
+                <option value="fixed" selected="True">Yes</option>
+                <option value="given">No, I want to keep the size of my peaks (-size given)</option>
+            </param>
+            <when value="given"/>
+            <when value="fixed">
+                <param argument="-size" type="integer" min="0" value="200" label="fragment size in bp"/>
+                <expand macro="choose_center"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1016/j.molcel.2010.05.004</citation>
+        </citations>
+    </xml>
+</macros>