Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 61:29fec32b8f47

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 12:59:20 -0400
parents 5c0901d0d8a8
children 770ce74dfc47
comparison
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60:5c0901d0d8a8 61:29fec32b8f47
20 ln -sf '$input_read_type_cond.input_pair[$key]['forward']' './cpipes-input/$read_R1'; 20 ln -sf '$input_read_type_cond.input_pair[$key]['forward']' './cpipes-input/$read_R1';
21 ln -sf '$input_read_type_cond.input_pair[$key]['reverse']' './cpipes-input/$read_R2'; 21 ln -sf '$input_read_type_cond.input_pair[$key]['reverse']' './cpipes-input/$read_R2';
22 #end for 22 #end for
23 #end if 23 #end if
24 $__tool_directory__/0.2.1/cpipes 24 $__tool_directory__/0.2.1/cpipes
25 --pipeline $input_read_type_cond.pipeline 25 --pipeline $input_read_type_cond.pipeline_cond.pipeline
26 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"): 26 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
27 --fq_single_end true 27 --fq_single_end true
28 --flye_genome_size '${genome_size}' 28 --flye_genome_size '${genome_size}'
29 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"): 29 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"):
30 --flye_nano_corr true --flye_nano_raw false 30 --flye_nano_corr true --flye_nano_raw false
60 rm -rf ./work || exit 1 60 rm -rf ./work || exit 1
61 ]]></command> 61 ]]></command>
62 <inputs> 62 <inputs>
63 <conditional name="input_read_type_cond"> 63 <conditional name="input_read_type_cond">
64 <param name="input_read_type" type="select" label="Select the read collection type"> 64 <param name="input_read_type" type="select" label="Select the read collection type">
65 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads/Long reads)</option> 65 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option>
66 <option value="paired">Paired-End reads</option> 66 <option value="paired">Paired-End reads</option>
67 </param> 67 </param>
68 <when value="single_long"> 68 <when value="single_long">
69 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" 69 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger"
70 label="Dataset list of unpaired short reads / long reads" /> 70 label="Dataset list of unpaired short reads or long reads" />
71 <conditional name="pipeline_cond"> 71 <conditional name="pipeline_cond">
72 <param name="pipeline" type="select" label="CPIPES Workflow name" 72 <param name="pipeline" type="select" label="CPIPES Workflow name"
73 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken"> 73 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken">
74 <option value="centriflaken" selected="true">centriflaken</option> 74 <option value="centriflaken" selected="true">centriflaken</option>
75 <option value="centriflaken_hy">centriflaken_hy</option> 75 <option value="centriflaken_hy">centriflaken_hy</option>