changeset 3:a539aeea69fc draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit ce0de4de3fa3fc25c375e378ac84f78452dd61c3

--- a/kraken-mpa-report.xml	Wed Jul 15 15:22:27 2015 -0400
+++ b/kraken-mpa-report.xml	Wed Aug 05 12:13:09 2015 -0400
@@ -1,38 +1,35 @@
-<tool id="kraken-mpa-report" name="Kraken-mpa-report" version="1.1.0">
-  <expand macro="version_command" />
-  <expand macro="requirements" />
-  <expand macro="stdio" />
-  <description>
-        view report of classification for multiple samples
-    </description>
+<?xml version="1.0"?>
+<tool id="kraken-mpa-report" name="Kraken-mpa-report" version="1.1.1">
+    <description>view report of classification for multiple samples</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
     <command>
-      <![CDATA[
+<![CDATA[
 
 #for $input_count, $input_classification in enumerate( $classification ):
- ln -s "${input_classification}" "sample_${input_count}" &&
+    ln -s "${input_classification}" "sample_${input_count}" &&
 #end for
 
-kraken-mpa-report @INPUT_DATABASE@
+@SET_DATABASE_PATH@ && kraken-mpa-report @INPUT_DATABASE@
 
 #for $input_count, $input_classification in enumerate( $classification ):
- "sample_${input_count}"
+    "sample_${input_count}"
 #end for
 
 ${show_zeros}
 ${header_line}
 
 > "$output_report"
-
-
-	]]>
+]]>
     </command>
     <inputs>
-      <param multiple="True" name="classification" type="data" format="tabular" label="Kraken output"/>
-      <param name="show_zeros" type="boolean" truevalue="--show-zeros" falsevalue="" checked="False" label="Display taxa even if they lack a read in any sample" help="--show-zeros"/>
-      <param name="header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="False" label="Display a header line indicating sample IDs" help="--header-line"/>
+        <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" />
+        <param checked="False" falsevalue="" help="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" />
+        <param checked="False" falsevalue="" help="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" />
         <expand macro="input_database" />
     </inputs>
     <outputs>
@@ -51,9 +48,9 @@
 
 Kraken-mpa-report summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple expreriments, conditions, locations, etc. It support sthe following parameters::
 
- --show-zeros    Display taxa even if they lack a read in any sample
- --header-line   Display a header line indicating sample IDs
-                 (sample IDs are the filenames)
+--show-zeros    Display taxa even if they lack a read in any sample
+--header-line   Display a header line indicating sample IDs
+                (sample IDs are the filenames)
 
 -----
 
@@ -61,11 +58,7 @@
 
 The output of kraken-mpa-report is tab-delimited, with one line per taxon.
 
-
-
-
-
-    ]]>
+]]>
     </help>
     <expand macro="citations" />
 </tool>