Mercurial > repos > iuc > umi_tools_extract

changeset 12:d5ff68d2d5ff draft

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"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
author iuc
date Tue, 10 Sep 2019 14:28:00 -0400
parents a472e995d157
children 6a675c3aa610
files macros.xml umi-tools_extract.xml
diffstat 2 files changed, 9 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Aug 27 17:10:51 2019 -0400
+++ b/macros.xml	Tue Sep 10 14:28:00 2019 -0400
@@ -3,8 +3,6 @@
     <macro name="barcode_sanitizer" >
         <sanitizer invalid_char="">
             <valid initial="string.letters,string.digits">
-                <add value="&#40;" /><!-- left bracket -->
-                <add value="&#41;" /><!-- right bracket -->
                 <add value="&#42;" /><!-- asterisk -->
                 <add value="&#44;" /><!-- comma -->
                 <add value="&#46;" /><!-- period -->
@@ -13,8 +11,15 @@
                 <add value="&#62;" /><!-- greater than -->
                 <add value="&#63;" /><!-- question mark -->
                 <add value="&#95;" /><!-- underscore -->
+                <add value="&#40;" /><!-- left bracket -->
+                <add value="&#41;" /><!-- right bracket -->
+                <add value="&#91;"/> <!-- left square bracket -->
+                <add value="&#93;"/> <!-- right square bracket -->
                 <add value="&#123;"/><!-- left brace -->
                 <add value="&#125;"/><!-- right brace -->
+                <add value="&#94;"/> <!-- caret -->
+                <add value="-"/>
+                <add value="!"/>
             </valid>
         </sanitizer>
     </macro>
--- a/umi-tools_extract.xml	Tue Aug 27 17:10:51 2019 -0400
+++ b/umi-tools_extract.xml	Tue Sep 10 14:28:00 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.0">
+<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.1">
     <description>Extract UMI from fastq files</description>
     <macros>
         <import>macros.xml</import>
@@ -105,24 +105,7 @@
                     represent the random positions and Xs to indicate the bc positions.
                     Bases with Ns will be extracted and added to the read name. Remaining
                     bases, marked with an X will be reattached to the read.">
-            <sanitizer invalid_char="">
-                <valid initial="string.letters,string.digits">
-                    <add value="!="/>
-                    <add value="-"/>
-                    <add value="_"/>
-                    <add value="."/>
-                    <add value="?"/>
-                    <add value="&lt;"/><!-- left triangle bracket -->
-                    <add value="&gt;"/><!-- right triangle bracket -->
-                    <add value="&#91;"/> <!-- left square bracket -->
-                    <add value="&#93;"/> <!-- right square bracket -->
-                    <add value="&#94;"/> <!-- caret -->
-                    <add value="&#123;"/> <!-- left curly -->
-                    <add value="&#125;"/> <!-- right curly -->
-                    <add value="&#40;"/> <!-- left parenthesis -->
-                    <add value="&#41;"/> <!-- right parenthesis -->
-                </valid>
-            </sanitizer>
+            <expand macro="barcode_sanitizer" />
         </param>
 
         <param name="prime3" argument="--3prime" type="boolean" label="Is the barcode at the 5' end?"