# HG changeset patch
# User youyuh48
# Date 1549354128 18000
# Node ID ccb90fac360530e7bd3747268c6e312ec7f9e5da
# Parent  d4372c7fa79d99b24a8850bc5a7d27883586301c
planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/centrifuge

diff -r d4372c7fa79d -r ccb90fac3605 centrifuge_kreport.xml
--- a/centrifuge_kreport.xml	Thu Aug 30 08:39:45 2018 -0400
+++ b/centrifuge_kreport.xml	Tue Feb 05 03:08:48 2019 -0500
@@ -1,48 +1,62 @@
 <tool id="centrifuge_kreport" name="centrifuge_kreport" version="0.1.0">
-    <description>Centrifuge-kreport creates Kraken-style reports from centrifuge out files</description>
-    <requirements>
-        <requirement type="package" version="1.0.3">centrifuge</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
+  <description>Centrifuge-kreport creates Kraken-style reports from centrifuge out files</description>
+  <requirements>
+    <requirement type="package" version="1.0.3">centrifuge</requirement>
+  </requirements>
+  <command detect_errors="exit_code">
+    <![CDATA[
         centrifuge-kreport
           -x '${db.fields.path}'
+
+          #if $settings.advanced == "advanced"
+            $settings.only_unique
+            $settings.show_zeros
+            $settings.count_table
+            --min-score $settings.min_score
+            --min-length $settings.min_length
+          #end if
+
           $input > output.txt
-    ]]></command>
-    <inputs>
-        <param type="data" name="input" format="tabular" />
-        <param name="db" type="select" label="Select a reference database">
-            <options from_data_table="centrifuge_indices">
-                <filter type="sort_by" column="2"/>
-                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
-            </options>
-        </param>
-    </inputs>
-    <outputs>
-        <data format="tsv" name="output" from_work_dir="output.txt" label="${tool.name} on ${on_string}" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" value="test-data_centrifuge-kreport/defaults.tsv"/>
-            <output name="output" file="defaults.tsv.kreport"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-Usage: centrifuge-kreport -x <index name> OPTIONS <centrifuge output file(s)>
-
+    ]]>
+  </command>
+  <inputs>
+    <param type="data" name="input" format="tabular"/>
+    <param name="db" type="select" label="Select a reference database">
+      <options from_data_table="centrifuge_indices">
+        <filter type="sort_by" column="2"/>
+  <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+</options>
+    </param>
+    <conditional name="settings">
+      <param name="advanced" type="select" label="Specify advanced parameters">
+        <option value="simple" selected="true">No, use program defaults.</option>
+        <option value="advanced">Yes, see full parameter list.</option>
+      </param>
+      <when value="simple"></when>
+      <when value="advanced">
+        <param name="only_unique" type="boolean" truevalue="--only-unique" falsevalue="" checked="false" label="Only count reads that were uniquely assigned to one taxon"/>
+        <param name="show_zeros" type="boolean" truevalue="--show-zeros" falsevalue="" checked="false" label="Show clades that have zero reads, too"/>
+        <param name="count_table" type="boolean" truevalue="--is-count-table" falsevalue="" label="The format of the file is 'TAXID-tab-COUNT' instead of the standard Centrifuge output format"/>
+        <param name="min_score" type="integer" label="--min-score" value="0" min="0" help="Require a minimum score for reads to be counted"/>
+        <param name="min_length" type="integer" label="--min-length" value="0" min="0" help="Require a minimum alignment length to the read"/>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output" from_work_dir="output.txt" label="${tool.name} on ${on_string}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="test-data_centrifuge-kreport/defaults.tsv"/>
+      <output name="output" file="defaults.tsv.kreport"/>
+    </test>
+  </tests>
+  <help>
+    <![CDATA[
 centrifuge-kreport creates Kraken-style reports from centrifuge out files.
-
-Options:
-    -x INDEX            (REQUIRED) Centrifuge index
-
-    --only-unique        Only count reads that were uniquely assigned to one taxon
-    --show-zeros         Show clades that have zero reads, too
-    --is-count-table     The format of the file is 'TAXID<tab>COUNT' instead of the standard
-                         Centrifuge output format
-
-    --min-score SCORE    Require a minimum score for reads to be counted
-    --min-length LENGTH  Require a minimum alignment length to the read
-    ]]></help>
-    <citations>
-        <citation type="doi">10.1101/gr.210641.116</citation>
-    </citations>
+    ]]>
+  </help>
+  <citations>
+    <citation type="doi">10.1101/gr.210641.116</citation>
+  </citations>
 </tool>