Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 85:022230c283f2

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 17:02:56 -0400
parents de5b87ce9fe4
children 7e421f421b5e
comparison
equal deleted inserted replaced
84:de5b87ce9fe4 85:022230c283f2
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 _, $unpaired in enumerate($input_read_type_cond.input): 12 #for _, $unpaired in enumerate($input_read_type_cond.input):
13 #set read1 = str($unpaired.name)
13 #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')): 14 #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')):
14 #set read1 = str($unpaired.name) + str('.') + str($unpaired.ext) 15 #set read1 = str($unpaired.name) + str('.') + str($unpaired.ext)
15 #else:
16 #set read1 = str($unpaired.name)
17 #end if 16 #end if
18 ln -sf '$unpaired' './cpipes-input/$read1'; 17 ln -sf '$unpaired' './cpipes-input/$read1';
19 #end for 18 #end for
20 #elif (str($input_read_type_cond.input_read_type) == "paired"): 19 #elif (str($input_read_type_cond.input_read_type) == "paired"):
21 #for _, $pair in enumerate($input_read_type_cond.input_pair) 20 #for _, $pair in enumerate($input_read_type_cond.input_pair)
22 #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext) 21 #set read_R1 = str($pair.forward.name)
23 #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext) 22 #set read_R2 = str($pair.reverse.name)
23 #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')):
24 #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext)
25 #end if
26 #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')):
27 #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext)
28 #end if
24 ln -sf '$pair.forward' './cpipes-input/$read_R1'; 29 ln -sf '$pair.forward' './cpipes-input/$read_R1';
25 ln -sf '$pair.reverse' './cpipes-input/$read_R2'; 30 ln -sf '$pair.reverse' './cpipes-input/$read_R2';
26 #end for 31 #end for
27 #end if 32 #end if
28 $__tool_directory__/0.2.1/cpipes 33 $__tool_directory__/0.2.1/cpipes
94 </when> 99 </when>
95 </conditional> 100 </conditional>
96 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Unpaired FASTQ"/> 101 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Unpaired FASTQ"/>
97 </when> 102 </when>
98 <when value="paired"> 103 <when value="paired">
99 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" 104 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="List of Dataset pairs" />
100 label="List of Dataset pairs" />
101 <conditional name="pipeline_cond"> 105 <conditional name="pipeline_cond">
102 <param name="pipeline" type="select" label="CPIPES Workflow name" 106 <param name="pipeline" type="select" label="CPIPES Workflow name"
103 help="Auto selected centriflaken_hy for paired-end short reads."> 107 help="Auto selected centriflaken_hy for paired-end short reads.">
104 <option value="centriflaken_hy" selected="true">centriflaken_hy</option> 108 <option value="centriflaken_hy" selected="true">centriflaken_hy</option>
105 </param> 109 </param>