Mercurial > repos > galaxy-australia > hifiadapterfilt

comparison hifiadapterfilt.xml @ 2:03acc0e3772e draft default tip

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"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
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1:41f5b4a4eac0 2:03acc0e3772e
8 </macros> 8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <command><![CDATA[ 11 <command><![CDATA[
12 12
13 @CLEAN_EXT@
14
15 #if $input_file.is_of_type("fastq.gz"): 13 #if $input_file.is_of_type("fastq.gz"):
16 #set $inputfile = $clean_ext($input_file.element_identifier) + '.fastq.gz' 14 #set $inputfile = "input" + '.fastq.gz'
17 #set prefix = $clean_ext($input_file.element_identifier) 15 #set prefix = "input"
18 #elif $input_file.is_of_type("fastq"): 16 #elif $input_file.is_of_type("fastq"):
19 #set $inputfile = $clean_ext($input_file.element_identifier) + '.fastq' 17 #set $inputfile = "input" + '.fastq'
20 #set prefix = $clean_ext($input_file.element_identifier) 18 #set prefix = "input"
21 #elif $input_file.is_of_type("bam"): 19 #elif $input_file.is_of_type("bam"):
22 #set $inputfile = $clean_ext($input_file.element_identifier) + '.bam' 20 #set $inputfile = "input" + '.bam'
23 #set prefix = $clean_ext($input_file.element_identifier) 21 #set prefix = "input"
24 #end if 22 #end if
25 ln -s '${input_file}' '${inputfile}' && 23 ln -s '${input_file}' '${inputfile}' &&
26 24
27 bash pbadapterfilt.sh 25 bash pbadapterfilt.sh
28 -p '$prefix' 26 -p '$prefix'
84 82
85 .. class:: infomark 83 .. class:: infomark
86 84
87 **Contributor** 85 **Contributor**
88 86
89 Galaxy Australia wrapped the HiFiadapterFilt: the original software is available in this Github repository `Github <https://github.com/sheinasim/HiFiAdapterFilt>`_. 87 Galaxy Australia wrapped the HiFiadapterFilt: the original software is available in this `Github repository <https://github.com/sheinasim/HiFiAdapterFilt>`_.
90 88
91 **References** 89 **References**
92 90
93 ]]></help> 91 ]]></help>
94 92