Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 75:eeddd4dfd7f5

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 16:23:56 -0400
parents 270e8f69228b
children 0e35724b49f0
comparison
equal deleted inserted replaced
74:270e8f69228b 75:eeddd4dfd7f5
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 #if (str($input_read_type_cond.input_read_type) == "single_long"): 11 #if (str($input_read_type_cond.input_read_type) == "single_long"):
12 #for $key in $input_read_type_cond.input.keys() 12 #for _, $unpaired in enumerate($input_read_type_cond.input):
13 ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key'; 13 #if not $unpaired.ext.endswith(('.fastq', '.fastq.gz')):
14 #set read_R1 = str($unpaired.name) + str($unpaired.ext)
15 #else:
16 #set read_R1 = str($unpaired.name)
17 #end if
18 ln -sf '$unpaired' './cpipes-input/$read_R1';
14 #end for 19 #end for
15 #elif (str($input_read_type_cond.input_read_type) == "paired"): 20 #elif (str($input_read_type_cond.input_read_type) == "paired"):
16 #for _, $pair in enumerate($input_read_type_cond.input_pair) 21 #for _, $pair in enumerate($input_read_type_cond.input_pair)
17 #set read_R1_name = str($pair.forward.name) 22 #set read_R1 = str($pair.forward.name) + str($pair.forward.ext)
18 #set read_R2_name = str($pair.reverse.name) 23 #set read_R2 = str($pair.reverse.name) + str($pair.reverse.ext)
19 ln -sf '$pair.forward' './cpipes-input/$read_R1_name'; 24 ln -sf '$pair.forward' './cpipes-input/$read_R1';
20 ln -sf '$pair.reverse' './cpipes-input/$read_R2_name'; 25 ln -sf '$pair.reverse' './cpipes-input/$read_R2';
21 #end for 26 #end for
22 #end if 27 #end if
23 $__tool_directory__/0.2.1/cpipes 28 $__tool_directory__/0.2.1/cpipes
24 --pipeline $input_read_type_cond.pipeline_cond.pipeline 29 --pipeline $input_read_type_cond.pipeline_cond.pipeline
25 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"): 30 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
63 <param name="input_read_type" type="select" label="Select the read collection type"> 68 <param name="input_read_type" type="select" label="Select the read collection type">
64 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option> 69 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option>
65 <option value="paired">Paired-End reads</option> 70 <option value="paired">Paired-End reads</option>
66 </param> 71 </param>
67 <when value="single_long"> 72 <when value="single_long">
68 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" 73 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz"
69 label="Dataset list of unpaired short reads or long reads" /> 74 label="Dataset list of unpaired short reads or long reads" />
70 <conditional name="pipeline_cond"> 75 <conditional name="pipeline_cond">
71 <param name="pipeline" type="select" label="CPIPES Workflow name" 76 <param name="pipeline" type="select" label="CPIPES Workflow name"
72 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken"> 77 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken">
73 <option value="centriflaken" selected="true">centriflaken</option> 78 <option value="centriflaken" selected="true">centriflaken</option>
89 </when> 94 </when>
90 </conditional> 95 </conditional>
91 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Unpaired FASTQ"/> 96 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Unpaired FASTQ"/>
92 </when> 97 </when>
93 <when value="paired"> 98 <when value="paired">
94 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" 99 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz"
95 label="List of Dataset pairs" /> 100 label="List of Dataset pairs" />
96 <conditional name="pipeline_cond"> 101 <conditional name="pipeline_cond">
97 <param name="pipeline" type="select" label="CPIPES Workflow name" 102 <param name="pipeline" type="select" label="CPIPES Workflow name"
98 help="Auto selected centriflaken_hy for paired-end short reads."> 103 help="Auto selected centriflaken_hy for paired-end short reads.">
99 <option value="centriflaken_hy" selected="true">centriflaken_hy</option> 104 <option value="centriflaken_hy" selected="true">centriflaken_hy</option>