changeset 2:cef64c36c89e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 0b535bf15f4bb0110f599c1af9b1dc1c66302899

--- a/README.rst	Wed Jul 27 09:26:36 2022 +0000
+++ b/README.rst	Tue Mar 12 08:50:50 2024 +0000
@@ -1,29 +1,7 @@
 Nonpareil memory usage
-=======================
+======================
 
 By default, this tool is configured to limit the memory consumption to 1024 Mib.
 
-Ideally this value should be larger than the sequences to analyze (discarding non-sequence elements like headers or quality). This is particularly important when running in multiple cores. This value is approximated. Maximum value in this version: 4194303.
-
-You can set the NONPAREIL_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file:
-
-```
-<?xml version="1.0"?>
-<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
-    </plugins>
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-    <destinations>
-        <destination id="local" runner="local">
-            <env id="NONPAREIL_MAX_MEMORY">1024</env>
-        </destination>
-    </destinations>
-</job_conf>
-```
-
-
-
+Ideally, this value should be larger than the sequences to analyze (discarding non-sequence elements like headers or quality). This is particularly important when running in multiple cores.
+This value is approximated. Maximum value in this version: 4194303.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Mar 12 08:50:50 2024 +0000
@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">nonpareil</requirement>
+    </requirements>
+  </xml>
+  <xml name="xrefs">
+    <xrefs>
+      <xref type="bio.tools">nonpareil</xref>
+    </xrefs>
+  </xml>
+  <token name="@TOOL_VERSION@">3.1.1</token>
+</macros>
\ No newline at end of file

--- a/nonpareil.xml	Wed Jul 27 09:26:36 2022 +0000
+++ b/nonpareil.xml	Tue Mar 12 08:50:50 2024 +0000
@@ -1,11 +1,10 @@
 <tool id="nonpareil" name="Nonpareil" version="@TOOL_VERSION@.1" profile="21.01">
     <description>to estimate average coverage and generate Nonpareil curves</description>
     <macros>
-        <token name="@TOOL_VERSION@">3.1.1</token>
+        <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">nonpareil</requirement>
-    </requirements>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <version_command>nonpareil -V</version_command>
     <command detect_errors="exit_code">
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