Mercurial > repos > greg > vsnp_sample_names

comparison vsnp_sample_names.xml @ 8:4f43f163c408 draft

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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit 9f80907d5bebf572ecd34e1171751c9091cb8697"
author greg
date Mon, 13 Sep 2021 19:35:10 +0000
parents e1cb13d6a82c
children
comparison
equal deleted inserted replaced
7:e1cb13d6a82c 8:4f43f163c408
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #import difflib 7 #import difflib
8 #import os
9 #import re 8 #import re
10 9
11 #if $input_type_cond.input_type == 'single': 10 #if $input_type_cond.input_type == 'single':
12 #set read1 = $input_type_cond.read1 11 #set read1 = $input_type_cond.read1
13 #set sample_name = re.sub('[^\s\w\-\\.]', '_', str($read1.element_identifier)) 12 #set sample_name = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
14 #else if $input_type_cond.input_type == 'pair': 13 #else if $input_type_cond.input_type == 'pair':
15 #set read1 = $input_type_cond.read1 14 #set read1 = $input_type_cond.read1
16 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) 15 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
17 #set read2 = $input_type_cond.read2 16 #set read2 = $input_type_cond.read2
18 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) 17 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
19 #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks() 18 #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks()
20 #set match = $matches[0] 19 #set match = $matches[0]
21 #set sample_name = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size])) 20 #set sample_name = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size]))
22 #else: 21 #else:
23 #set read1 = $input_type_cond.reads_collection['forward'] 22 #set read1_name = $input_type_cond.reads_collection['forward'].name
24 #set read1_filename = $read1.name 23 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1_name))
25 #set sample_name = re.sub('[^\s\w\-]', '_', str($read1_filename)) 24 #set read2_name = $input_type_cond.reads_collection['reverse'].name
26 #end if 25 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2_name))
27 26 #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks()
28 #if $sample_name.find('_R1') >0: 27 #set match = $matches[0]
29 ## Something like CMC_20E1_R1.fastq.gz 28 #set sample_name = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size]))
30 #set sample_name = $sample_name.split('_R1')[0]
31 #else if $sample_name.find(".") > 0:
32 #if $read1.is_of_type('fastqsanger.gz') and $sample_name.endswith('gz'):
33 ## Something like my_sample.fastq.gz
34 #set sample_name = '.'.join($sample_name.split('.')[0:-2])
35 #else:
36 ## Something like my_sample.fastq
37 #set sample_name = $os.path.splitext($sample_name)[0]
38 #end if
39 #else if $sample_name.find("_") > 0:
40 #if $read1.is_of_type('fastqsanger.gz') and $sample_name.endswith('gz'):
41 ## Something like my_sample_fastq_gz
42 #set sample_name = '_'.join($sample_name.split('_')[0:-2])
43 #else:
44 ## Something like my_sample_fastq
45 #set sample_name = "_".join($sample_name.split("_")[0:-1])
46 #end if
47 #end if 29 #end if
48 30
49 echo '$sample_name' > '$output' 31 echo '$sample_name' > '$output'
50 ]]></command> 32 ]]></command>
51 <inputs> 33 <inputs>
80 <!-- Paired reads in separate datasets --> 62 <!-- Paired reads in separate datasets -->
81 <test> 63 <test>
82 <param name="input_type" value="pair"/> 64 <param name="input_type" value="pair"/>
83 <param name="read1" value="CMC_20E1_R1.fastq.gz" dbkey="89"/> 65 <param name="read1" value="CMC_20E1_R1.fastq.gz" dbkey="89"/>
84 <param name="read2" value="CMC_20E1_R2.fastq.gz" dbkey="89"/> 66 <param name="read2" value="CMC_20E1_R2.fastq.gz" dbkey="89"/>
85 <output name="output" file="sample_names.txt" ftype="txt"/> 67 <output name="output" file="sample_names2.txt" ftype="txt"/>
86 </test> 68 </test>
87 <!-- Collection of Paired reads --> 69 <!-- Collection of Paired reads -->
88 <test> 70 <test>
89 <param name="input_type" value="paired"/> 71 <param name="input_type" value="paired"/>
90 <param name="reads_collection"> 72 <param name="reads_collection">
91 <collection type="paired"> 73 <collection type="paired">
92 <element name="forward" value="CMC_20E1_R1.fastq.gz"/> 74 <element name="forward" value="CMC_20E1_R1.fastq.gz"/>
93 <element name="reverse" value="CMC_20E1_R2.fastq.gz"/> 75 <element name="reverse" value="CMC_20E1_R2.fastq.gz"/>
94 </collection> 76 </collection>
95 </param> 77 </param>
96 <output name="output" file="sample_names.txt" ftype="txt"/> 78 <output name="output" file="sample_names3.txt" ftype="txt"/>
97 </test> 79 </test>
98 <!-- Collection of Paired reads --> 80 <!-- Collection of Paired reads -->
99 <test> 81 <test>
100 <param name="input_type" value="paired"/> 82 <param name="input_type" value="paired"/>
101 <param name="reads_collection"> 83 <param name="reads_collection">
102 <collection type="paired"> 84 <collection type="paired">
103 <element name="forward" value="SRR14085881_forward"/> 85 <element name="forward" value="SRR14085881_forward"/>
104 <element name="reverse" value="SRR14085881_reverse"/> 86 <element name="reverse" value="SRR14085881_reverse"/>
105 </collection> 87 </collection>
106 </param> 88 </param>
107 <output name="output" file="sample_names2.txt" ftype="txt"/> 89 <output name="output" file="sample_names4.txt" ftype="txt"/>
108 </test> 90 </test>
109 </tests> 91 </tests>
110 <help> 92 <help>
111 **What it does** 93 **What it does**
112 94