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annotate hicup_macros.xml @ 0:396bdc215399 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
author bgruening
date Mon, 24 Oct 2022 15:58:52 +0000
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children 82641e9a86cb
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396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
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1 <macros>
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2 <token name="@VERSION@">0.8.3</token>
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3 <xml name="requirements_hicup">
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4 <requirements>
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5 <requirement type="package" version="@VERSION@">hicup</requirement>
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6 <requirement type="package" version="2.4.5">bowtie2</requirement>
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7 <requirement type="package" version="1.16.1">samtools</requirement>
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8 <yield/>
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9 </requirements>
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10 <version_command>hicup --version</version_command>
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11 </xml>
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12 <xml name="citation_hicup">
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13 <citations>
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14 <citation type="doi">10.12688/f1000research.7334.1</citation>
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15 </citations>
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16 </xml>
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17 <xml name="reference_genome_macro">
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18 <conditional name="reference_genome">
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19 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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20 <option value="indexed">Use a built-in genome index</option>
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21 <option value="history">Use a genome from the history and build index</option>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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22 </param>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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23 <when value="indexed">
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24 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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25 <options from_data_table="bowtie2_indexes">
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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26 <filter type="sort_by" column="2"/>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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27 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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28 </options>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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29 </param>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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30 </when>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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31 <when value="history">
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32 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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33 <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />-->
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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34 </when>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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35 </conditional>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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36 </xml>
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37 <xml name="re1">
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38 <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme used e.g. A^GATCT,BglII. Some Hi-C protocols may use several enzymes. To specify several enzymes, use the ':' to separate them e.g. A^GATCT,BglII:A^AGCTT,HindIII:^GATC,DpnII. HiCUP accomodates N in restriction enzyme: e.g. :A^ANCTT"/>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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39 </xml>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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40 <xml name="re2">
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41 <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags."
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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42 help="To specify a restriction enzyme instead of sonication to shorten di-tags. This restriction site does NOT form a Hi-C ligation junction. 2 .g. AG^CT,AluI. Typically the sonication protocol is followed."/>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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43 </xml>
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44 <xml name="filter_longest_shortest">
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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45 <param argument="--longest" type="text" value="" label="Max insert size" help="Maximum allowable insert size (bps)"/>
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46 <param argument="--shortest" type="text" value="" label="Min insert size" help="Minimum allowable insert size (bps)"/>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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47 </xml>
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48 <xml name="no_fill">
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49 <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill"
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50 help="Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence"/>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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51 </xml>
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52 <token name="@PAIRED-END_INPUT@"><![CDATA[
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53 ## Taken from cutadapt except that I don't accept space in name
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54 #import re
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55 #set library_type = str($library.type)
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56 #if $library_type == 'paired':
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57 #set input_1 = $library.input_1
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58 #set input_2 = $library.input_2
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59 #else if $library_type == 'paired_collection'
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60 #set input_1 = $library.input_1.forward
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61 #set input_2 = $library.input_1.reverse
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62 #end if
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63
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64 #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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65 #set ext = ".fq.gz"
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66 #else:
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67 #set ext = ".fq"
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68 #end if
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69 #set read1 = "dataset1" + $ext
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70 ln -f -s '${input_1}' '$read1' &&
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71
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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72 #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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73 #set ext2 = ".fq.gz"
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74 #else:
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75 #set ext2 = ".fq"
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76 #end if
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77 #set read2 = "dataset2" + $ext2
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78 ln -f -s '${input_2}' '$read2' &&
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79 ]]>
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80 </token>
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81 <xml name="input_paired">
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82 <conditional name="library">
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83 <param name="type" type="select" label="How Paired-end reads are organized">
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84 <option value="paired">Separately</option>
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85 <option value="paired_collection">Paired-end Collection</option>
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86 </param>
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87
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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88 <when value="paired">
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89 <param name="input_1" format="fastq,fastq.gz" type="data" label="FASTQ/A file #1" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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90 <param name="input_2" format="fastq,fastq.gz" type="data" label="FASTQ/A file #2" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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91 </when>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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92
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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93 <when value="paired_collection">
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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94 <param name="input_1" format="fastq,fastq.gz" type="data_collection" collection_type="paired" label="Paired Collection" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fastq&quot;" />
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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95 </when>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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96
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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97 </conditional>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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98 </xml>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
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99 </macros>