Mercurial > repos > greg > vsnp_sample_names
comparison vsnp_sample_names.xml @ 0:f75e2ac7b6cd draft
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author | greg |
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date | Tue, 21 Apr 2020 10:17:20 -0400 |
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children | 895d18fcfebe |
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-1:000000000000 | 0:f75e2ac7b6cd |
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1 <tool id="vsnp_sample_names" name="vSNP: sample names" version="1.0.0"> | |
2 <description></description> | |
3 <command detect_errors="exit_code"><![CDATA[ | |
4 #import os | |
5 #import re | |
6 #set output_dir = 'output' | |
7 mkdir -p $output_dir | |
8 #if str($input_type_cond.input_type) == "single": | |
9 ## We may have a single read or a pair, but in | |
10 ## either case we want the same base file name. | |
11 #set sample_name = $os.path.basename($input_type_cond.read.element_identifier) | |
12 #if $sample_name.find(".") > 0: | |
13 #set sample_name = $sample_name.split(".")[0] | |
14 #end if | |
15 #if $sample_name.find("_") > 0: | |
16 #set sample_name = $sample_name.split("_")[0] | |
17 #end if | |
18 echo $sample_name > $output | |
19 #else: | |
20 #for $i in $input_type_cond.reads_collection: | |
21 #set sample_name = $os.path.basename($i.element_identifier) | |
22 #if $sample_name.find(".") > 0: | |
23 #set sample_name = $sample_name.split(".")[0] | |
24 #end if | |
25 #set output_file = $os.path.join($output_dir, $sample_name) | |
26 && echo $sample_name > $output_file | |
27 #end for | |
28 #end if | |
29 ]]></command> | |
30 <inputs> | |
31 <conditional name="input_type_cond"> | |
32 <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> | |
33 <option value="single" selected="true">Single files</option> | |
34 <option value="collection">Collections of files</option> | |
35 </param> | |
36 <when value="single"> | |
37 <param name="read" type="data" format="fastqsanger.gz,fastqsanger" label="Sample file"/> | |
38 </when> | |
39 <when value="collection"> | |
40 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Collection of sample files"/> | |
41 </when> | |
42 </conditional> | |
43 </inputs> | |
44 <outputs> | |
45 <data name="output" format="txt"> | |
46 <filter>input_type_cond['input_type'] == 'single'</filter> | |
47 </data> | |
48 <collection name="output__collection" type="list"> | |
49 <discover_datasets pattern="__name__" directory="output" format="txt" /> | |
50 <filter>input_type_cond['input_type'] == 'collection'</filter> | |
51 </collection> | |
52 </outputs> | |
53 <tests> | |
54 <test> | |
55 <param name="input_type" value="collection"/> | |
56 <param name="reads_collection"> | |
57 <collection type="list"> | |
58 <element name="BCG_Danish_Human_UK_SRR9596061.fastq" value="BCG_Danish_Human_UK_SRR9596061.fastq" dbkey="89"/> | |
59 <element name="Dassie_Dassie_ZA_SRR3745455.fastq" value="Dassie_Dassie_ZA_SRR3745455.fastq" dbkey="89"/> | |
60 <element name="Mbov_Cattle_NI_SRR10993937.fastq" value="Mbov_Cattle_NI_SRR10993937.fastq" dbkey="89"/> | |
61 </collection> | |
62 </param> | |
63 <output_collection name="output__collection" type="list"> | |
64 <element name="BCG_Danish_Human_UK_SRR9596061" file="BCG_Danish_Human_UK_SRR9596061" ftype="txt"/> | |
65 <element name="Dassie_Dassie_ZA_SRR3745455" file="Dassie_Dassie_ZA_SRR3745455" ftype="txt"/> | |
66 <element name="Mbov_Cattle_NI_SRR10993937" file="Mbov_Cattle_NI_SRR10993937" ftype="txt"/> | |
67 </output_collection> | |
68 </test> | |
69 </tests> | |
70 <help> | |
71 **What it does** | |
72 | |
73 Accepts one or more sample files and extracts a unique portion of the file name as the content of the output file(s). These | |
74 text files are then used as workflow parameter values for the Read Group Identifier parameter in the bwa-mem tool. | |
75 | |
76 **Required Options** | |
77 | |
78 * **Choose the category of the files to be analyzed** - select "Single files" or "Collections of files", then select the appropriate history items (single or paired fastqsanger reads or collections of fastqsanger reads) based on the selected option. | |
79 </help> | |
80 <citations> | |
81 <citation type="bibtex"> | |
82 @misc{None, | |
83 journal = {None}, | |
84 author = {1. Stuber T}, | |
85 title = {Manuscript in preparation}, | |
86 year = {None}, | |
87 url = {https://github.com/USDA-VS/vSNP},} | |
88 </citation> | |
89 </citations> | |
90 </tool> | |
91 |