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comparison hicup_macros.xml @ 5:2edfb71706b3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
author bgruening
date Sat, 22 Oct 2022 08:41:11 +0000
parents a2f3a4129052
children e79c38f1752c
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4:a2f3a4129052 5:2edfb71706b3
1 <macros> 1 <macros>
2 <token name="@VERSION@">0.6.1</token> 2 <token name="@VERSION@">0.8.3</token>
3 <xml name="requirements_hicup"> 3 <xml name="requirements_hicup">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="@VERSION@">hicup</requirement> 5 <requirement type="package" version="@VERSION@">hicup</requirement>
6 <requirement type="package" version="2.2.6">bowtie2</requirement> 6 <requirement type="package" version="2.4.5">bowtie2</requirement>
7 <requirement type="package" version="1.2">samtools</requirement> 7 <requirement type="package" version="1.16.1">samtools</requirement>
8 <requirement type="package" version="0.13.1">docutils</requirement>
9 <yield/> 8 <yield/>
10 </requirements> 9 </requirements>
11 <version_command>hicup --version</version_command> 10 <version_command>hicup --version</version_command>
12 </xml> 11 </xml>
13 <xml name="citation_hicup"> 12 <xml name="citation_hicup">
33 <param name="own_file" type="data" format="fasta" label="Select reference genome" /> 32 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
34 <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />--> 33 <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />-->
35 </when> 34 </when>
36 </conditional> 35 </conditional>
37 </xml> 36 </xml>
38 <xml name="input_files">
39 <param name="input_first_sequence" type="data" format="fastq,fastq.gz" label="First input sequence" help="The first sequence:"/>
40 <param name="input_second_sequence" type="data" format="fastq,fastq.gz" label="Second input sequence" help="The second sequence:"/>
41 </xml>
42 <xml name="re1"> 37 <xml name="re1">
43 <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme recognition sequence"/> 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"/>
44 </xml> 39 </xml>
45 <xml name="re2"> 40 <xml name="re2">
46 <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags." 41 <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags."
47 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."/> 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."/>
48 </xml> 43 </xml>
52 </xml> 47 </xml>
53 <xml name="no_fill"> 48 <xml name="no_fill">
54 <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill" 49 <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill"
55 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"/> 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"/>
56 </xml> 51 </xml>
52 <token name="@PAIRED-END_INPUT@"><![CDATA[
53 ## Taken from cutadapt except that I don't accept space in name
54 #import re
55 #set library_type = str($library.type)
56 #if $library_type == 'paired':
57 #set input_1 = $library.input_1
58 #set input_2 = $library.input_2
59 #else if $library_type == 'paired_collection'
60 #set input_1 = $library.input_1.forward
61 #set input_2 = $library.input_1.reverse
62 #end if
63
64 #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
65 #set ext = ".fq.gz"
66 #else:
67 #set ext = ".fq"
68 #end if
69 #set read1 = "dataset1" + $ext
70 ln -f -s '${input_1}' '$read1' &&
71
72 #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
73 #set ext2 = ".fq.gz"
74 #else:
75 #set ext2 = ".fq"
76 #end if
77 #set read2 = "dataset2" + $ext2
78 ln -f -s '${input_2}' '$read2' &&
79 ]]>
80 </token>
81 <xml name="input_paired">
82 <conditional name="library">
83 <param name="type" type="select" label="How Paired-end reads are organized">
84 <option value="paired">Separately</option>
85 <option value="paired_collection">Paired-end Collection</option>
86 </param>
87
88 <when value="paired">
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;" />
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;" />
91 </when>
92
93 <when value="paired_collection">
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;" />
95 </when>
96
97 </conditional>
98 </xml>
57 </macros> 99 </macros>