changeset 2:2bd5a88cd70d draft

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bracken commit 53ace3bf562db4907cfb239ef7699de04dc6ff6e-dirty

--- a/est-abundance.xml	Tue May 21 12:42:49 2019 -0400
+++ b/est-abundance.xml	Thu May 25 13:42:42 2023 +0000
@@ -5,19 +5,20 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-    est_abundance.py 
+    bracken \\ 
     -i '$input' 
-    -k $kmer_distr 
+    -d '$kmer_distr.fields.path' 
     -l $level 
-    -t $threshold 
+    -t $threshold
     -o '$report'
+    -w '$kreport'
     ]]>
     </command>
     
     <inputs>
         <param name="input" type="data" format="tabular" label="Kraken report file" />
         <param label="Select a Kmer distribution" name="kmer_distr" type="select">
-            <options from_data_table="bracken_databases">
+            <options from_data_table="new_bracken_databases">
                 <validator message="No database is available" type="no_options" />
             </options>
         </param>
@@ -30,20 +31,25 @@
             <option value="P">Phylum</option>
             <option value="D">Domain</option>
         </param>
+        <param name="read_len" type="select" label="Read length" help="Read length to get all classifications for">
+            <option value="150" selected="true">150</option>
+            <option value="200">200</option>
+            <option value="250">250</option>
+            <option value="300">300</option>
+        </param>
         <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag" help="Threshold for the minimum number of reads kraken must
                         assign to a classification for that classification to
                         be considered in the final abundance estimation." />
-        
     </inputs>
 
     <outputs>
-        <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
+        <data name="report" format="tabular" label="${tool.name} on ${on_string}: Bracken Report" />
+        <data name="kreport" format="tabular" label="${tool.name} on ${on_string}: Kraken Report by Bracken" />
     </outputs>
 
     <expand macro="citations" />    
     <help>
     <![CDATA[
-
         Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_.
     ]]></help>
 

--- a/macros.xml	Tue May 21 12:42:49 2019 -0400
+++ b/macros.xml	Thu May 25 13:42:42 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">2.2</token>
+    <token name="@VERSION@">2.8</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">bracken</requirement>

--- a/tool-data/bracken_databases.loc.sample	Tue May 21 12:42:49 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-# This file defines databases and their folder location. Each database is a line with 
-# three columns: value{tab}{name}{/path/to/database-file} 
-# E.g. database100mers{tab}database100mers{tab}/home/user/bracken_databases/database100mers.kmer_distrib

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/new_bracken_databases.loc.sample	Thu May 25 13:42:42 2023 +0000
@@ -0,0 +1,3 @@
+# This file defines databases and their folder location. Each database is a line with 
+# three columns: value{tab}{name}{/path/to/database-file} 
+# E.g. database100mers{tab}database100mers{tab}/home/user/bracken_databases/database100mers.kmer_distrib

--- a/tool_data_table_conf.xml.sample	Tue May 21 12:42:49 2019 -0400
+++ b/tool_data_table_conf.xml.sample	Thu May 25 13:42:42 2023 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of ariba database in the required format -->
-    <table name="bracken_databases" comment_char="#" allow_duplicate_entries="False">
+    <table name="new_bracken_databases" comment_char="#" allow_duplicate_entries="False">
         <columns>value, name, path</columns>
-        <file path="tool-data/bracken_databases.loc" />
+        <file path="tool-data/new_bracken_databases.loc" />
     </table>
 </tables>
\ No newline at end of file