Mercurial > repos > galaxy-australia > hifiadapterfilt
changeset 2:03acc0e3772e draft default tip
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit db087ed782a52833a02df3bfef0793b4dd909081"
| author | galaxy-australia |
|---|---|
| date | Wed, 16 Nov 2022 06:19:15 +0000 |
| parents | 41f5b4a4eac0 |
| children | |
| files | hifiadapterfilt.xml macros.xml |
| diffstat | 2 files changed, 7 insertions(+), 21 deletions(-) [+] |
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--- a/hifiadapterfilt.xml Wed Sep 14 02:37:39 2022 +0000 +++ b/hifiadapterfilt.xml Wed Nov 16 06:19:15 2022 +0000 @@ -10,17 +10,15 @@ <expand macro="stdio" /> <command><![CDATA[ - @CLEAN_EXT@ - #if $input_file.is_of_type("fastq.gz"): - #set $inputfile = $clean_ext($input_file.element_identifier) + '.fastq.gz' - #set prefix = $clean_ext($input_file.element_identifier) + #set $inputfile = "input" + '.fastq.gz' + #set prefix = "input" #elif $input_file.is_of_type("fastq"): - #set $inputfile = $clean_ext($input_file.element_identifier) + '.fastq' - #set prefix = $clean_ext($input_file.element_identifier) + #set $inputfile = "input" + '.fastq' + #set prefix = "input" #elif $input_file.is_of_type("bam"): - #set $inputfile = $clean_ext($input_file.element_identifier) + '.bam' - #set prefix = $clean_ext($input_file.element_identifier) + #set $inputfile = "input" + '.bam' + #set prefix = "input" #end if ln -s '${input_file}' '${inputfile}' && @@ -86,7 +84,7 @@ **Contributor** -Galaxy Australia wrapped the HiFiadapterFilt: the original software is available in this Github repository `Github <https://github.com/sheinasim/HiFiAdapterFilt>`_. +Galaxy Australia wrapped the HiFiadapterFilt: the original software is available in this `Github repository <https://github.com/sheinasim/HiFiAdapterFilt>`_. **References**
--- a/macros.xml Wed Sep 14 02:37:39 2022 +0000 +++ b/macros.xml Wed Nov 16 06:19:15 2022 +0000 @@ -14,16 +14,4 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> - <token name="@CLEAN_EXT@"> - <![CDATA[ - #from os.path import splitext - #import re - #def clean_ext($identifier) - #while $identifier.endswith(('.fq','.fastq', '.fastq.gz','.bam')) - #set $identifier = splitext($identifier)[0] - #end while -$identifier#slurp - #end def - ]]> - </token> </macros>