Mercurial > repos > iuc > umi_tools_count

changeset 5:933220bbc2ae draft

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"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
author iuc
date Tue, 10 Sep 2019 14:28:47 -0400
parents 70cb5527defb
children 276b4111b253
files macros.xml umi-tools_counts.xml
diffstat 2 files changed, 9 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Aug 27 17:11:32 2019 -0400
+++ b/macros.xml	Tue Sep 10 14:28:47 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_counts.xml	Tue Aug 27 17:11:32 2019 -0400
+++ b/umi-tools_counts.xml	Tue Sep 10 14:28:47 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.0">
+<tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.1">
     <description>performs quantification of UMIs from BAM files</description>
     <macros>
         <import>macros.xml</import>
@@ -102,24 +102,7 @@
                 <expand macro="sanitize_tag" />
             </param>
             <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
-                <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 argument="--per-contig" name="per_contig" type="boolean" truevalue="--per-contig" falsevalue="" checked="false" label="Deduplicate per contig (field 3 in BAM; RNAME)"  help="All reads with the same contig will be considered to have the same alignment position. This is useful if you have aligned to a reference transcriptome with one transcript per gene." />
             <param argument="--per-cell" name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" checked="true" label="Group reads only if they have the same cell barcode." />