Mercurial > repos > jdv > albacore

diff albacore_1D.xml @ 8:3dfde840119e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
author jdv
date Mon, 18 Jun 2018 12:20:28 -0400
parents 4d72adba794f
children
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--- a/albacore_1D.xml	Sat Mar 10 15:43:07 2018 -0500
+++ b/albacore_1D.xml	Mon Jun 18 12:20:28 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="albacore_1D" name="Albacore 1D" version="2.0.2">
+<tool id="albacore_1D" name="Albacore 1D" version="2.0.2b">
 
     <description>ONT production basecaller</description>
 
@@ -6,7 +6,7 @@
    
     <!--
     <requirements>
-        <requirement type="package" version="1.2.6">albacore</requirement>
+        <requirement type="package" version="2.0.2">albacore</requirement>
     </requirements>
     -->
 
@@ -19,7 +19,7 @@
     <command detect_errors="aggressive">
     <![CDATA[
 
-    python3 $__tool_directory__/albacore_1D.py $input $output $out_format $demux \${GALAXY_SLOTS:-1}
+    python3 $__tool_directory__/albacore_1D.py $input $output $out_format $demux $disable_filt \${GALAXY_SLOTS:-1}
 
     ]]>
     </command>
@@ -34,6 +34,7 @@
             <option value="fast5">fast5</option>
         </param>
         <param name="demux" type="boolean" checked="false" label="Demultiplex" />
+        <param name="disable_filt" type="boolean" checked="false" label="Disable quality filtering" />
         <param name="output_table" type="boolean" checked="false" label="Include table in output" />
 
     </inputs>
@@ -56,7 +57,6 @@
             <filter>demux is True and out_format == 'fast5'</filter>
             <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fast5.tar.gz" />
         </collection>
-
         <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${tool.name} on ${on_string} (table)">
             <filter>output_table is True</filter>
         </data>
@@ -70,6 +70,11 @@
             <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
             <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
         </test>
+        <test>
+            <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
+            <param name="disable_filt" value="true" />
+            <output name="output" file="test_data_nofilt.fastq" compare="sim_size" delta="0"/>
+        </test>
     </tests>
 
     <!-- ***************************************************************** -->