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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/misc/sample_names commit b935f36cfe430263564503ebb71f78dc79315acb"
author greg
date Mon, 22 Nov 2021 00:30:39 +0000
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54380a6171b8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/misc/sample_names commit b935f36cfe430263564503ebb71f78dc79315acb"
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1 <tool id="sample_names" name="Extract sample names" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>from input file names</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #import difflib
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8 #import re
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9
54380a6171b8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/misc/sample_names commit b935f36cfe430263564503ebb71f78dc79315acb"
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10 #if $input_type_cond.input_type == 'single':
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11 #set read1 = $input_type_cond.read1
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12 #set sample_name = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
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13 #else if $input_type_cond.input_type == 'pair':
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14 #set read1 = $input_type_cond.read1
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15 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
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16 #set read2 = $input_type_cond.read2
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17 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
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18 #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks()
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19 #set match = $matches[0]
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20 #set sample_name = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size]))
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21 #else:
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22 #set read1_name = $input_type_cond.reads_collection['forward'].name
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23 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1_name))
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24 #set read2_name = $input_type_cond.reads_collection['reverse'].name
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25 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2_name))
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26 #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks()
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27 #set match = $matches[0]
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28 #set sample_name = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size]))
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29 #end if
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30
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31 echo '$sample_name' > '$output'
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32 ]]></command>
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33 <inputs>
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34 <conditional name="input_type_cond">
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35 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
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36 <option value="single" selected="true">Single dataset</option>
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37 <option value="pair">Dataset pair</option>
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38 <option value="paired">List of dataset pairs</option>
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39 </param>
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40 <when value="single">
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41 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
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42 </when>
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43 <when value="pair">
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44 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
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45 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
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46 </when>
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47 <when value="paired">
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48 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
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49 </when>
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50 </conditional>
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51 </inputs>
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52 <outputs>
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53 <data name="output" format="txt"/>
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54 </outputs>
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55 <tests>
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56 <!-- Single files -->
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57 <test>
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58 <param name="input_type" value="single"/>
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59 <param name="read1" value="CMC_20E1_R1.fastq.gz" dbkey="89"/>
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60 <output name="output" file="sample_names.txt" ftype="txt"/>
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61 </test>
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62 <!-- Paired reads in separate datasets -->
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63 <test>
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64 <param name="input_type" value="pair"/>
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65 <param name="read1" value="CMC_20E1_R1.fastq.gz" dbkey="89"/>
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66 <param name="read2" value="CMC_20E1_R2.fastq.gz" dbkey="89"/>
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67 <output name="output" file="sample_names2.txt" ftype="txt"/>
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68 </test>
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69 <!-- Collection of Paired reads -->
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70 <test>
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71 <param name="input_type" value="paired"/>
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72 <param name="reads_collection">
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73 <collection type="paired">
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74 <element name="forward" value="CMC_20E1_R1.fastq.gz"/>
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75 <element name="reverse" value="CMC_20E1_R2.fastq.gz"/>
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76 </collection>
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77 </param>
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78 <output name="output" file="sample_names3.txt" ftype="txt"/>
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79 </test>
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80 <!-- Collection of Paired reads -->
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81 <test>
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82 <param name="input_type" value="paired"/>
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83 <param name="reads_collection">
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84 <collection type="paired">
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85 <element name="forward" value="SRR14085881_forward"/>
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86 <element name="reverse" value="SRR14085881_reverse"/>
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87 </collection>
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88 </param>
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89 <output name="output" file="sample_names4.txt" ftype="txt"/>
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90 </test>
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91 </tests>
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92 <help>
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93 **What it does**
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94
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95 Accepts fastqsanger sample files, extracts a unique portion of the file name as the sample name, and writes it to
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96 the output. The output text file can be consumed by the **Parse parameter value** expression tool to provide workflow
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97 parameter values to the **Read group identifier (ID)** and the **Sample name identifier (SM)** parameters in the
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98 **Map with BWA-MEM** tool.
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99 </help>
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100 <expand macro="citations"/>
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101 </tool>
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102