Mercurial > repos > artbio > guppy_basecaller

changeset 4:bc53d2ba84c4 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit 690e93e439c4e1ba442ae53576095444d82df34f"
author artbio
date Sat, 28 Nov 2020 15:25:16 +0000
parents df3f2f852ed5
children dd0cccf3a62f
files guppy_basecaller.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/guppy_basecaller.xml	Sat Nov 28 15:12:30 2020 +0000
+++ b/guppy_basecaller.xml	Sat Nov 28 15:25:16 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.6" python_template_version="3.5">
+<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.2.0" python_template_version="3.5">
     <description>A simple wrapper for guppy basecaller that depends on configuration files</description>
     <requirements>
     </requirements>
@@ -18,14 +18,14 @@
                          --disable_pings
 ###                         --qscore_filtering
 ###                         --calib_detect
-        && cat *.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output.fastq
+        && cat *.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output_fastq
     ]]></command>
     <inputs>
         <param name="infiles" type="data_collection" format="h5" label="Fast5 input (datatype h5)" multiple="true"/>
         <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/>
     </inputs>
     <outputs>
-        <data name="output.fastq" format="fastqsanger" />
+        <data name="output_fastq" format="fastqsanger" />
     </outputs>
     <help><![CDATA[
         A wrapper for guppy basecaller. This expects two type of inputs: a collection of fast5 files,