Mercurial > repos > kkonganti > cfsan_centriflaken
comparison cfsan_centriflaken.xml @ 85:022230c283f2
"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> |