Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 67:04c9f550eb08

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 13:55:47 -0400
parents ccc58509834c
children 44d4e4078aaa
comparison
equal deleted inserted replaced
66:ccc58509834c 67:04c9f550eb08
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 $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 $read_R1 = os.path.basename(str($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 $read_R2 = os.path.basename(str($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';
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"):
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"> 97 <conditional name="pipeline_cond">
98 <param name="pipeline" type="select" label="CPIPES Workflow name" 98 <param name="pipeline" type="select" label="CPIPES Workflow name"
99 help="centriflaken_hy selected for paired-end short reads."> 99 help="Auto selected centriflaken_hy for paired-end short reads.">
100 <option value="centriflaken_hy" selected="true">centriflaken_hy</option> 100 <option value="centriflaken_hy" selected="true">centriflaken_hy</option>
101 </param> 101 </param>
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."/>