Mercurial > repos > iuc > umi_tools_dedup

changeset 9:1692b1acebfd draft

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"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
author iuc
date Tue, 10 Sep 2019 14:28:24 -0400
parents 983ec27dce7c
children c6567483aa1e
files macros.xml umi-tools_dedup.xml
diffstat 2 files changed, 8 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Aug 27 17:11:11 2019 -0400
+++ b/macros.xml	Tue Sep 10 14:28:24 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_dedup.xml	Tue Aug 27 17:11:11 2019 -0400
+++ b/umi-tools_dedup.xml	Tue Sep 10 14:28:24 2019 -0400
@@ -34,7 +34,7 @@
                 --in-sam
             #end if
             -I '$input_file' -S deduped.bam &&
-            samtools sort deduped.bam -@ \${GALAXY_SLOTS:-1} -o '$output' -O BAM
+            samtools sort deduped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM
     ]]></command>
     <inputs>
         <param name="input" type="data" format="sam,bam" label="Reads to deduplicate in SAM or BAM format" />