Mercurial > repos > iuc > crossmap_region

diff macros.xml @ 0:8635b6b8a8f2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
author iuc
date Thu, 15 Jul 2021 16:19:33 +0000
parents
children eb66d7a04bf8
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,49 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">crossmap</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">0.5.2</token>
+    <token name="@VERSION_SUFFIX@">0</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><![CDATA[
+CrossMap.py 2>&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_data_table="liftOver">
+                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="input_chain" type="data" format="txt" label="LiftOver chain file"/>
+            </when>
+        </conditional>
+    </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>