diff macros.xml @ 0:bc72094f7ce9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Sep 26 05:44:37 2017 -0400
@@ -0,0 +1,56 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="324">ucsc-wigtobigwig</requirement>
+            <requirement type="package" version="0.2.2">crossmap</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@WRAPPER_VERSION@">0.2.2</token>
+    <xml name="stdio">
+        <stdio>
+            <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
+            <regex match=".*" source="both" level="log"/>
+            <exit_code range="1:"/>
+        </stdio>
+    </xml>
+    <xml name="version_command">
+        <version_command>CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
+    </xml>
+    <xml name="chain">
+        <conditional name="chain_source">
+            <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
+                <option value="cached">Local data (in galaxy)</option>
+                <option value="history">From History</option>
+            </param>
+            <when value="cached">
+                <param name="input_chain" type="select" label="Lift Over To">
+                    <options from_file="liftOver.loc">
+                        <column name="dbkey" index="0"/><!-- species/build 'from' -->
+                        <column name="name" index="1"/><!-- species/build 'to' -->
+                        <column name="value" index="2"/><!-- path of chain file -->
+                        <filter type="data_meta" ref="input" key="dbkey" column="0"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="source">
+        <param name="index_source" type="select" label="Source for Input Data">
+            <option value="cached">Local data (in galaxy)</option>
+            <option value="history">From History</option>
+        </param>
+    </xml>
+    <token name="@HELP_GENERAL@">
+CrossMap
+--------
+CrossMap is versatile tool to convert genome coordinates or annotation files between genome
+assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
+GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
+and VCF, reading from remote servers and file compression are supported.
+    </token>
+</macros>