Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 66:ccc58509834c

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 13:47:12 -0400
parents ec3fca35a622
children 04c9f550eb08
comparison
equal deleted inserted replaced
65:ec3fca35a622 66:ccc58509834c
11 #import os 11 #import os
12 #if (str($input_read_type_cond.input_read_type) == "single_long"): 12 #if (str($input_read_type_cond.input_read_type) == "single_long"):
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/$key';
15 #end for 15 #end for
16 #else: 16 #elif (str($input_read_type_cond.input_read_type) == "paired"):
17 #for $key in $input_read_type_cond.input_pair.keys() 17 #for $key in $input_read_type_cond.input_pair.keys()
18 #set $read_R1 = os.path.basename($input_read_type_cond.input_pair[$key]['forward']) 18 #set $read_R1 = os.path.basename($input_read_type_cond.input_pair[$key]['forward'])
19 #set $read_R2 = os.path.basename($input_read_type_cond.input_pair[$key]['reverse']) 19 #set $read_R2 = os.path.basename($input_read_type_cond.input_pair[$key]['reverse'])
20 ln -sf '$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';
92 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/> 92 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
93 </when> 93 </when>
94 <when value="paired"> 94 <when value="paired">
95 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" 95 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger"
96 label="List of Dataset pairs" /> 96 label="List of Dataset pairs" />
97 <conditional name="pipeline_cond">
98 <param name="pipeline" type="select" label="CPIPES Workflow name"
99 help="centriflaken_hy selected for paired-end short reads.">
100 <option value="centriflaken_hy" selected="true">centriflaken_hy</option>
101 </param>
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"
104 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."/>
105 </when>
106 </conditional>
97 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/> 107 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
98 <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"/>
99 </when> 109 </when>
100 </conditional> 110 </conditional>
101 <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"