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comparison rgFastQC.xml @ 17:c15237684a01 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit e06f74f574276b793bf9c1c788de8d97db449af2
author iuc
date Fri, 01 Jun 2018 15:49:50 -0400
parents ff9530579d1f
children 3e1cdf5406db
comparison
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16:ff9530579d1f 17:c15237684a01
1 <tool id="fastqc" name="FastQC" version="0.71"> 1 <tool id="fastqc" name="FastQC" version="0.72">
2 <description>Read Quality reports</description> 2 <description>Read Quality reports</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.11.6">fastqc</requirement> 4 <requirement type="package" version="0.11.7">fastqc</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #import re 7 #import re
8 #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier)) 8 #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier))
9 9
10 #if $input_file.ext.endswith('.gz'): 10 #if $input_file.ext.endswith('.gz'):
11 #set input_file_sl = $input_name + '.gz' 11 #set input_file_sl = $input_name + '.gz'
12 #elif $input_file.ext.endswith('.bz2'): 12 #elif $input_file.ext.endswith('.bz2'):
13 #set input_file_sl = $input_name + '.bz2' 13 #set input_file_sl = $input_name + '.bz2'
14 #else 14 #else
25 25
26 ln -s '${input_file}' '${input_file_sl}' && 26 ln -s '${input_file}' '${input_file_sl}' &&
27 mkdir -p '${html_file.files_path}' && 27 mkdir -p '${html_file.files_path}' &&
28 fastqc 28 fastqc
29 --outdir '${html_file.files_path}' 29 --outdir '${html_file.files_path}'
30 30
31 #if $contaminants.dataset and str($contaminants) > '' 31 #if $contaminants.dataset and str($contaminants) > ''
32 --contaminants '${contaminants}' 32 --contaminants '${contaminants}'
33 #end if 33 #end if
34 34
35 #if $limits.dataset and str($limits) > '' 35 #if $limits.dataset and str($limits) > ''
36 --limits '${limits}' 36 --limits '${limits}'
37 #end if 37 #end if
38 38
39 --quiet 39 --quiet
40 --extract 40 --extract
41 -f '${format}' 41 -f '${format}'
42 '${input_file_sl}' 42 '${input_file_sl}'
43 43