annotate vsnp_sample_names.xml @ 1:895d18fcfebe draft

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author greg
date Tue, 27 Oct 2020 18:21:55 +0000
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1 <tool id="vsnp_sample_names" name="vSNP: sample names" version="1.0.0">
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2 <description></description>
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3 <command detect_errors="exit_code"><![CDATA[
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4 #import os
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5 #import re
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6 #set output_dir = 'output'
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7 mkdir -p $output_dir &&
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8 #if str($input_type_cond.input_type) == "single":
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9 ## We may have a single read or a pair, but in
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10 ## either case we want the same base file name.
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11 #set sample_name = $os.path.basename($input_type_cond.read.element_identifier)
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12 #if $sample_name.find(".") > 0:
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13 #set sample_name = $sample_name.split(".")[0]
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14 #end if
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15 #if $sample_name.find("_") > 0:
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16 #set sample_name = $sample_name.split("_")[0]
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17 #end if
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18 && echo '$sample_name' > '$output'
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19 #else:
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20 #for $i in $input_type_cond.reads_collection:
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21 #set sample_name = $os.path.basename($i.element_identifier)
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22 #if $sample_name.find(".") > 0:
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23 #set sample_name = $sample_name.split(".")[0]
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24 #end if
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25 #set output_file = $os.path.join($output_dir, $sample_name)
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26 && echo '$sample_name' > '$output_file'
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27 #end for
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28 #end if
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29 ]]></command>
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30 <inputs>
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31 <conditional name="input_type_cond">
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32 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
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33 <option value="single" selected="true">Single files</option>
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34 <option value="collection">Collections of files</option>
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35 </param>
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36 <when value="single">
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37 <param name="read" type="data" format="fastqsanger.gz,fastqsanger" label="Sample file"/>
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38 </when>
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39 <when value="collection">
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40 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Collection of sample files"/>
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41 </when>
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42 </conditional>
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43 </inputs>
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44 <outputs>
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45 <data name="output" format="txt">
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46 <filter>input_type_cond['input_type'] == 'single'</filter>
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47 </data>
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48 <collection name="output__collection" type="list">
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49 <discover_datasets pattern="__name__" directory="output" format="txt" />
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50 <filter>input_type_cond['input_type'] == 'collection'</filter>
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51 </collection>
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="input_type" value="collection"/>
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56 <param name="reads_collection">
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57 <collection type="list">
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58 <element name="BCG_Danish_Human_UK_SRR9596061.fastq" value="BCG_Danish_Human_UK_SRR9596061.fastq" dbkey="89"/>
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59 <element name="Dassie_Dassie_ZA_SRR3745455.fastq" value="Dassie_Dassie_ZA_SRR3745455.fastq" dbkey="89"/>
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60 <element name="Mbov_Cattle_NI_SRR10993937.fastq" value="Mbov_Cattle_NI_SRR10993937.fastq" dbkey="89"/>
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61 </collection>
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62 </param>
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63 <output_collection name="output__collection" type="list">
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64 <element name="BCG_Danish_Human_UK_SRR9596061" file="BCG_Danish_Human_UK_SRR9596061" ftype="txt"/>
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65 <element name="Dassie_Dassie_ZA_SRR3745455" file="Dassie_Dassie_ZA_SRR3745455" ftype="txt"/>
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66 <element name="Mbov_Cattle_NI_SRR10993937" file="Mbov_Cattle_NI_SRR10993937" ftype="txt"/>
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67 </output_collection>
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68 </test>
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69 </tests>
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70 <help>
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71 **What it does**
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72
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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
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74 text files are then used as workflow parameter values for the Read Group Identifier parameter in the bwa-mem tool.
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75
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76 **Required Options**
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77
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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.
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79 </help>
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80 <citations>
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81 <citation type="bibtex">
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82 @misc{None,
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83 journal = {None},
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84 author = {1. Stuber T},
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85 title = {Manuscript in preparation},
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86 year = {None},
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87 url = {https://github.com/USDA-VS/vSNP},}
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88 </citation>
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89 </citations>
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90 </tool>
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91