Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 105:52045ea4679d

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"planemo upload"
author kkonganti
date Thu, 27 Jun 2024 14:17:26 -0400
parents 96a34c382154
children c02d3cf60fe0
comparison
equal deleted inserted replaced
104:17890124001d 105:52045ea4679d
1 <tool id="cfsan_centriflaken" name="Centriflaken" version="0.2.0+galaxy0"> 1 <tool id="cfsan_centriflaken" name="Centriflaken" version="0.4.1+galaxy1">
2 <description>An automated pipeline to generate a MAG of interest (E.coli or Salmonella) and perform serotyping.</description> 2 <description>An automated pipeline to generate a MAG of interest (E.coli or Salmonella) and perform serotyping.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="22.04">nextflow</requirement> 4 <requirement type="package" version="24.04">nextflow</requirement>
5 <requirement type="package">graphviz</requirement> 5 <requirement type="package">graphviz</requirement>
6 </requirements> 6 </requirements>
7 <version_command>nextflow -version</version_command> 7 <version_command>nextflow -version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 mkdir -p cpipes-input || exit 1; 9 mkdir -p cpipes-input || exit 1;
10 pwd_path=\$(pwd); 10 pwd_path=\$(pwd);
11 time_stamp=\$(date +%Y-%m-%d-%s);
12 work_dir="\${pwd_path}/centriflaken_work_dir-"\${time_stamp};
13 mkdir -p \$work_dir || exit 1;
11 #import re 14 #import re
12 #if (str($input_read_type_cond.input_read_type) == "single_long"): 15 #if (str($input_read_type_cond.input_read_type) == "single_long"):
13 #for _, $unpaired in enumerate($input_read_type_cond.input): 16 #for _, $unpaired in enumerate($input_read_type_cond.input):
14 #set read1 = str($unpaired.name) 17 #set read1 = str($unpaired.name)
15 #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')): 18 #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')):
32 #end if 35 #end if
33 ln -sf '$pair.forward' './cpipes-input/$read_R1'; 36 ln -sf '$pair.forward' './cpipes-input/$read_R1';
34 ln -sf '$pair.reverse' './cpipes-input/$read_R2'; 37 ln -sf '$pair.reverse' './cpipes-input/$read_R2';
35 #end for 38 #end for
36 #end if 39 #end if
37 $__tool_directory__/0.4.0/cpipes 40 $__tool_directory__/0.4.2/cpipes
38 --pipeline $input_read_type_cond.pipeline_cond.pipeline 41 --pipeline $input_read_type_cond.pipeline_cond.pipeline
39 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"): 42 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
40 --fq_single_end true 43 --fq_single_end true
41 --flye_genome_size '${genome_size}' 44 --flye_genome_size '${genome_size}'
42 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"): 45 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"):