changeset 3:9bdcba262627 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_translate/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd

--- a/kraken-translate.xml	Wed Mar 23 11:02:57 2016 -0400
+++ b/kraken-translate.xml	Mon Aug 07 17:29:45 2017 -0400
@@ -1,26 +1,29 @@
-<tool id="kraken-translate" name="Kraken-translate" version="1.2.1">
-    <description>
-        convert taxonomy IDs to names
-    </description>
+<tool id="kraken-translate" name="Kraken-translate" version="@WRAPPER_VERSION@">
+    <description>convert taxonomy IDs to names</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
-        <![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
         @SET_DATABASE_PATH@ &&
-        kraken-translate @INPUT_DATABASE@ $mpa_format "${input}" > "${translated}"
-        ]]>
-    </command>
+
+        kraken-translate
+            @INPUT_DATABASE@
+            $mpa_format
+            '${input}'
+            > '${translated}'
+    ]]></command>
     <inputs>
-        <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/>
-        <param label="Restrict labels to standard rank assignments" name="mpa_format" truevalue="--mpa-format" falsevalue="" type="boolean" />
+        <param name="input" type="data" format="tabular" label="Kraken output"
+               help="Select taxonomy classification produced by kraken"/>
+        <param name="mpa_format" type="boolean" truevalue="--mpa-format" falsevalue=""
+               label="Restrict labels to standard rank assignments" />
+
         <expand macro="input_database" />
     </inputs>
     <outputs>
-        <data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />
+        <data name="translated" format="tabular" label="${tool.name} on ${on_string}: Translated classification"/>
     </outputs>
     <tests>
         <test>
@@ -30,8 +33,7 @@
             <output name="translated" file="kraken_translate_test1_output.tab" ftype="tabular"/>
         </test>
     </tests>
-    <help>
-        <![CDATA[
+    <help><![CDATA[
 
 .. class:: warningmark
 
@@ -54,7 +56,6 @@
  SEQ1  d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli
 
 Taxonomy assignments above the superkingdom rank are represented as just "root" when using the ``--mpa-report`` option with kraken-translate.
-        ]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>

--- a/macros.xml	Wed Mar 23 11:02:57 2016 -0400
+++ b/macros.xml	Mon Aug 07 17:29:45 2017 -0400
@@ -1,23 +1,20 @@
 <?xml version="1.0"?>
 <macros>
+    <token name="@WRAPPER_VERSION@">1.2.3</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement>
-            <requirement type="package" version="0.10.6-eaf8fb68">kraken</requirement>
         </requirements>
     </xml>
-    <xml name="stdio">
-        <stdio>
-            <exit_code description="Tool exception" level="fatal" range="1:" />
-        </stdio>
-    </xml>
     <xml name="version_command">
-        <version_command>export LC_ALL=C &amp;&amp; kraken --version</version_command>
+        <version_command><![CDATA[
+            export LC_ALL=C && kraken --version
+        ]]></version_command>
     </xml>
     <xml name="input_database">
         <param label="Select a Kraken database" name="kraken_database" type="select">
             <options from_data_table="kraken_databases">
-                <validator message="No databases are available built-in" type="no_options" />
+                <validator message="No Kraken database is available" type="no_options" />
             </options>
         </param>
     </xml>
@@ -28,4 +25,4 @@
     </xml>
     <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token>
     <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token>
-</macros>
\ No newline at end of file
+</macros>

--- a/tool_dependencies.xml	Wed Mar 23 11:02:57 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="kraken" version="0.10.6-eaf8fb68">
-      <repository changeset_revision="0743afe4dcb8" name="package_kraken_0_10_6_eaf8fb68" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>