# HG changeset patch
# User iuc
# Date 1502141269 14400
# Node ID ccfb9cbfcc72526acaaabf42349f665f6fbc61f4
# Parent  d246279116a47d4b83c01535609cb57819a11b4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_filter/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd

diff -r d246279116a4 -r ccfb9cbfcc72 kraken-filter.xml
--- a/kraken-filter.xml	Wed Mar 23 10:59:52 2016 -0400
+++ b/kraken-filter.xml	Mon Aug 07 17:27:49 2017 -0400
@@ -1,22 +1,24 @@
-<tool id="kraken-filter" name="Kraken-filter" version="1.2.1">
-    <description>
-        filter classification by confidence score
-    </description>
+<tool id="kraken-filter" name="Kraken-filter" version="@WRAPPER_VERSION@">
+    <description>filter classification by confidence score</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-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output"
-        ]]>
-    </command>
+
+        kraken-filter
+            @INPUT_DATABASE@
+            --threshold $threshold
+            '${input}'
+            > '$filtered_output'
+    ]]></command>
     <inputs>
-        <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/>
-        <param label="Confidence threshold" max="1" min="0" name="threshold" type="float" value="0" help="--threshold; A number between 0 and 1; default=0"/>
+        <param name="input" type="data" format="tabular" label="Kraken output" help="Select taxonomy classification produced by kraken"/>
+        <param argument="--threshold" type="float" value="0" min="0" max="1"
+               label="Confidence threshold" help="A floating point number between 0 and 1; default=0"/>
+
         <expand macro="input_database" />
     </inputs>
     <outputs>
@@ -27,7 +29,8 @@
             <param name="input" value="kraken_filter_test1.tab"/>
             <param name="threshold" value="0"/>
             <param name="kraken_database" value="test_db"/>
-            <output name="output" file="kraken_filter_test1_output.tab" ftype="tabular"/>
+
+            <output name="filtered_output" file="kraken_filter_test1_output.tab" ftype="tabular"/>
         </test>
     </tests>
 
@@ -46,7 +49,7 @@
 
 A sequence label's score is a fraction C/Q, where C is the number of k-mers mapped to LCA values in the clade rooted at the label, and Q is the number of k-mers in the sequence that lack an ambiguous nucleotide (i.e., they were queried against the database). Consider the example of the LCA mappings in Kraken's output::
 
- 562:13 561:4 A:31 0:1 562:3 
+ 562:13 561:4 A:31 0:1 562:3
 
 would indicate that::
 
diff -r d246279116a4 -r ccfb9cbfcc72 macros.xml
--- a/macros.xml	Wed Mar 23 10:59:52 2016 -0400
+++ b/macros.xml	Mon Aug 07 17:27:49 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>
diff -r d246279116a4 -r ccfb9cbfcc72 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 23 10:59:52 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="6dc210626044" name="package_kraken_0_10_6_eaf8fb68" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>