Mercurial > repos > cjav > split_by_barcode

changeset 5:1506445d0665 draft

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New way of providing barcodes to use. Using ngs-tools==0.1.5.
author cjav
date Mon, 16 Sep 2013 14:36:09 -0400
parents f40640700846
children 9b59d2017dd6
files ngs-tools_split_by_barcode.xml tool_dependencies.xml
diffstat 2 files changed, 8 insertions(+), 10 deletions(-) [+]
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line diff
--- a/ngs-tools_split_by_barcode.xml	Fri Sep 06 14:15:03 2013 -0400
+++ b/ngs-tools_split_by_barcode.xml	Mon Sep 16 14:36:09 2013 -0400
@@ -1,15 +1,15 @@
-<tool id="ngs-tools_split_by_barcode" name="Barcode Splitter (ngs-tools)" force_history_refresh="True">
+<tool id="ngs-tools_split_by_barcode" name="Barcode Splitter (ngs-tools)" force_history_refresh="True" version="1.0.1">
 	<description></description>
     <requirements>
-        <requirement type="package" version="0.1.4">ngs-tools</requirement>
+        <requirement type="package" version="0.1.5">ngs-tools</requirement>
     </requirements>
     <command>
         ngs-tools split-by-barcode
             $trim_barcode $input_format.format
             --barcode-size $barcode_length --max-distance $max_distance
-            #for $i in $barcodes
-              --barcode ${i.barcode}
-            #end for
+            #if $barcodes
+              --barcodes $barcodes
+            #end if
             --report $output1 --galaxy $output1.id --output $__new_file_path__
             $barcode_index
             #for $i in $input_format.inputs
@@ -36,9 +36,7 @@
         </conditional>
         <param format="tabular" name="barcode_index" type="data" label="Barcodes index" help="See below for description." />
         <param name="barcode_length" type="integer" size="3" value="11" label="Barcode length" help="Please specify the barcode length." />
-        <repeat name="barcodes" title="Barcode" help="Barcodes to use. By default all barcodes with the correct length in the index are used. By using this option you can limit which ones to use.">
-            <param name="barcode" type="text" label="Barcode to use" />
-        </repeat>
+        <param name="barcodes" type="text" label="Barcodes to use" help="Comma separated list of barcodes to use. By default all barcodes in the 'Barcodes index' are used." />
         <param name="trim_barcode" type="select" label="Trim the barcode" help="By default barcodes are trimmed from the resulting splitted datasets">
             <option value="" selected="true">Yes</option>
             <option value="--keep-barcode">No</option>
--- a/tool_dependencies.xml	Fri Sep 06 14:15:03 2013 -0400
+++ b/tool_dependencies.xml	Mon Sep 16 14:36:09 2013 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="ngs-tools" version="0.1.4">
-        <repository changeset_revision="f95c90140890" name="package_ngs_tools_0_1_4" owner="cjav" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="ngs-tools" version="0.1.5">
+        <repository changeset_revision="df1454bc4a5e" name="package_ngs_tools_0_1_5" owner="cjav" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>