Mercurial > repos > iuc > umi_tools_group

annotate macros.xml @ 8:aa5ec9b8c99a draft

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planemo upload commit a7a086ce7d7d84f53d4a022fa1da25ef7b9a5b9a
author iuc
date Fri, 20 Jul 2018 03:48:54 -0400
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children 3b8fecdf9058
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1 <?xml version="1.0"?>
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2 <macros>
3
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3 <macro name="barcode2_conditional" >
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4 <conditional name="barcode">
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5 <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?">
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6 <option value="first_read_only">Barcode on first read only</option>
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7 <option value="both_reads">Barcode on both reads</option>
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8 </param>
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9 <when value="first_read_only"/>
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10 <when value="both_reads">
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11 <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
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12 help="Use this option to specify the format of the UMI/barcode for
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13 the second read pair if required." >
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14 </param>
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15 </when>
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16 </conditional>
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17 </macro>
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18 <xml name="input_types">
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19 <conditional name="input_type">
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20 <param name="type" type="select" label="Library type">
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21 <option value="single">Single-end</option>
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22 <option value="paired">Paired-end</option>
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23 <option value="paired_collection">Paired-end Dataset Collection</option>
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24 </param>
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25 <when value="single">
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26 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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27 </when>
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28 <when value="paired">
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29 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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30 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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31 <expand macro="barcode2_conditional" />
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32 </when>
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33 <when value="paired_collection">
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34 <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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35 <expand macro="barcode2_conditional" />
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36 </when>
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37 </conditional>
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38 </xml>
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39 <xml name="citations">
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40 <citations>
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41 <citation type="doi">10.1101/gr.209601.116</citation>
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42 <citation type="bibtex">
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43 @misc{githubUMI-tools,
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44 title = {UMI-tools},
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45 publisher = {GitHub},
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46 journal = {GitHub repository},
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47 url = {https://github.com/CGATOxford/UMI-tools},
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48 }
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49 </citation>
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50 </citations>
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51 </xml>
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52 <xml name="requirements">
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53 <requirements>
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54 <requirement type="package" version="@VERSION@">umi_tools</requirement>
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55 <yield />
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56 </requirements>
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57 </xml>
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58 <token name="@VERSION@">0.5.3</token>
3
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59 <token name="@COMMAND_LINK@"><![CDATA[
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60 #set $gz = False
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61 #if $input_type.type == 'single':
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62 #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
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63 ln -s '$input_type.input_single' input_single.gz &&
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64 #set $gz = True
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65 #else
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66 ln -s '$input_type.input_single' input_single.txt &&
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67 #end if
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68 #elif $input_type.type == 'paired':
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69 #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
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70 ln -s '$input_type.input_read1' input_read1.gz &&
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71 ln -s '$input_type.input_read2' input_read2.gz &&
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72 #set $gz = True
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73 #else
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74 ln -s '$input_type.input_read1' input_read1.txt &&
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75 ln -s '$input_type.input_read2' input_read2.txt &&
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76 #end if
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77 #else ## paired_collection
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78 #if $input_type.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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79 ln -s '$input_type.input_readpair.forward' input_read1.gz &&
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80 ln -s '$input_type.input_readpair.reverse' input_read2.gz &&
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81 #set $gz = True
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82 #else
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83 ln -s '$input_type.input_readpair.forward' input_read1.txt &&
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84 ln -s '$input_type.input_readpair.reverse' input_read2.txt &&
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85 #end if
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86 #end if
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87 ]]></token>
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88 </macros>