Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 70:4e72dfe54475

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 14:13:16 -0400
parents 905def920829
children 783721d5b326
comparison
equal deleted inserted replaced
69:905def920829 70:4e72dfe54475
13 #for $key in $input_read_type_cond.input.keys() 13 #for $key in $input_read_type_cond.input.keys()
14 ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key'; 14 ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key';
15 #end for 15 #end for
16 #elif (str($input_read_type_cond.input_read_type) == "paired"): 16 #elif (str($input_read_type_cond.input_read_type) == "paired"):
17 #for _, $pair in enumerate($input_read_type_cond.input_pair) 17 #for _, $pair in enumerate($input_read_type_cond.input_pair)
18 #set $read_R1 = os.path.basename(str(${pair.forward})) 18 #set $read_R1 = os.path.basename(str($pair.forward))
19 #set $read_R2 = os.path.basename(str(${pair.reverse})) 19 #set $read_R2 = os.path.basename(str($pair.reverse))
20 ln -sf '${pair.forward}' './cpipes-input/${read_R1.name}'; 20 ln -sf '$pair.forward' './cpipes-input/${read_R1.name}';
21 ln -sf '${pair.reverse}' './cpipes-input/${read_R2.name}'; 21 ln -sf '$pair.reverse' './cpipes-input/${read_R2.name}';
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_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"):
102 <when value="centriflaken_hy"> 102 <when value="centriflaken_hy">
103 <param name="long_read_platform" value="N/A" type="text" optional="true" label="Mention long read sequencing platform and type" 103 <param name="long_read_platform" value="N/A" type="text" optional="true" label="Mention long read sequencing platform and type"
104 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."/> 104 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."/>
105 </when> 105 </when>
106 </conditional> 106 </conditional>
107 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/> 107 <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
108 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/> 108 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/>
109 </when> 109 </when>
110 </conditional> 110 </conditional>
111 <param name="fq_filter_by_len" optional="true" value="" type="integer" label="Enter minimum read length to retain before starting the analysis" 111 <param name="fq_filter_by_len" optional="true" value="" type="integer" label="Enter minimum read length to retain before starting the analysis"
112 help="Keep this option empty to use default values. Default for centriflaken (long reads) is 4000 bp and for centriflaken_hy (short reads) is 75 bp."/> 112 help="Keep this option empty to use default values. Default for centriflaken (long reads) is 4000 bp and for centriflaken_hy (short reads) is 75 bp."/>