Mercurial > repos > iuc > umi_tools_group

annotate macros.xml @ 9:3b8fecdf9058 draft

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"planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
author iuc
date Tue, 27 Aug 2019 17:10:29 -0400
parents 7d886fe41f56
children a24f5b991320
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1 <?xml version="1.0"?>
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2 <macros>
9
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3 <macro name="barcode_sanitizer" >
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4 <sanitizer invalid_char="">
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5 <valid initial="string.letters,string.digits">
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6 <add value="&#40;" /><!-- left bracket -->
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7 <add value="&#41;" /><!-- right bracket -->
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8 <add value="&#42;" /><!-- asterisk -->
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9 <add value="&#44;" /><!-- comma -->
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10 <add value="&#46;" /><!-- period -->
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11 <add value="&#60;" /><!-- less than -->
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12 <add value="&#61;" /><!-- equals sign -->
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13 <add value="&#62;" /><!-- greater than -->
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14 <add value="&#63;" /><!-- question mark -->
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15 <add value="&#95;" /><!-- underscore -->
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16 <add value="&#123;"/><!-- left brace -->
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17 <add value="&#125;"/><!-- right brace -->
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18 </valid>
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19 </sanitizer>
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20 </macro>
3
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21 <macro name="barcode2_conditional" >
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22 <conditional name="barcode">
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23 <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?">
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24 <option value="first_read_only">Barcode on first read only</option>
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25 <option value="both_reads">Barcode on both reads</option>
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26 </param>
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27 <when value="first_read_only"/>
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28 <when value="both_reads">
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29 <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
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30 help="Use this option to specify the format of the UMI/barcode for
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31 the second read pair if required." >
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32 <expand macro="barcode_sanitizer" />
3
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33 </param>
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34 </when>
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35 </conditional>
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36 </macro>
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37 <xml name="input_types">
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38 <conditional name="input_type">
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39 <param name="type" type="select" label="Library type">
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40 <option value="single">Single-end</option>
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41 <option value="paired">Paired-end</option>
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42 <option value="paired_collection">Paired-end Dataset Collection</option>
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43 </param>
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44 <when value="single">
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45 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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46 </when>
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47 <when value="paired">
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48 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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49 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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50 <expand macro="barcode2_conditional" />
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51 </when>
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52 <when value="paired_collection">
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53 <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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54 <expand macro="barcode2_conditional" />
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55 </when>
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56 </conditional>
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57 </xml>
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58 <xml name="citations">
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59 <citations>
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60 <citation type="doi">10.1101/gr.209601.116</citation>
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61 <citation type="bibtex">
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62 @misc{githubUMI-tools,
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63 title = {UMI-tools},
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64 publisher = {GitHub},
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65 journal = {GitHub repository},
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66 url = {https://github.com/CGATOxford/UMI-tools},
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67 }
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68 </citation>
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69 </citations>
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70 </xml>
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71 <xml name="requirements">
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72 <requirements>
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73 <requirement type="package" version="@VERSION@">umi_tools</requirement>
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74 <yield />
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75 </requirements>
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76 </xml>
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77 <token name="@VERSION@">0.5.5</token>
3
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78 <token name="@COMMAND_LINK@"><![CDATA[
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79 #set $gz = False
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80 #if $input_type.type == 'single':
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81 #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
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82 ln -s '$input_type.input_single' input_single.gz &&
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83 #set $gz = True
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84 #else
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85 ln -s '$input_type.input_single' input_single.txt &&
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86 #end if
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87 #elif $input_type.type == 'paired':
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88 #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
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89 ln -s '$input_type.input_read1' input_read1.gz &&
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90 ln -s '$input_type.input_read2' input_read2.gz &&
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91 #set $gz = True
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92 #else
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93 ln -s '$input_type.input_read1' input_read1.txt &&
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94 ln -s '$input_type.input_read2' input_read2.txt &&
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95 #end if
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96 #else ## paired_collection
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97 #if $input_type.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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98 ln -s '$input_type.input_readpair.forward' input_read1.gz &&
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99 ln -s '$input_type.input_readpair.reverse' input_read2.gz &&
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100 #set $gz = True
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101 #else
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102 ln -s '$input_type.input_readpair.forward' input_read1.txt &&
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103 ln -s '$input_type.input_readpair.reverse' input_read2.txt &&
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104 #end if
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105 #end if
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106 ]]></token>
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107 </macros>