Mercurial > repos > bgruening > hicup_mapper

annotate hicup_macros.xml @ 7:be104dee2833 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17
author bgruening
date Thu, 23 Feb 2023 18:07:06 +0000
parents 396e8c4ebfee
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
1 <macros>
7
be104dee2833 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17
bgruening
parents: 5
diff changeset
2 <token name="@VERSION@">0.9.2</token>
2
320a2d826a00 planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit c546c919808a853d3e1556cb28bb4a5f7e1f9932
bgruening
parents: 1
diff changeset
3 <xml name="requirements_hicup">
0
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
4 <requirements>
2
320a2d826a00 planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit c546c919808a853d3e1556cb28bb4a5f7e1f9932
bgruening
parents: 1
diff changeset
5 <requirement type="package" version="@VERSION@">hicup</requirement>
5
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
6 <requirement type="package" version="2.4.5">bowtie2</requirement>
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
7 <requirement type="package" version="1.16.1">samtools</requirement>
7
be104dee2833 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17
bgruening
parents: 5
diff changeset
8 <!-- without this dependency, hicup_hicup could not generate the html
be104dee2833 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17
bgruening
parents: 5
diff changeset
9 The error is: /usr/local/bin/pandoc: error while loading shared libraries: libgmp.so.10: cannot open shared object file: No such file or directory -->
be104dee2833 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17
bgruening
parents: 5
diff changeset
10 <requirement type="package" version="6.2.1">gmp</requirement>
4
99dd0efa992b planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
bgruening
parents: 3
diff changeset
11 <yield/>
0
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
12 </requirements>
4
99dd0efa992b planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
bgruening
parents: 3
diff changeset
13 <version_command>hicup --version</version_command>
0
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
14 </xml>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
15 <xml name="citation_hicup">
4
99dd0efa992b planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
bgruening
parents: 3
diff changeset
16 <citations>
99dd0efa992b planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
bgruening
parents: 3
diff changeset
17 <citation type="doi">10.12688/f1000research.7334.1</citation>
99dd0efa992b planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
bgruening
parents: 3
diff changeset
18 </citations>
0
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
19 </xml>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
20 <xml name="reference_genome_macro">
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
21 <conditional name="reference_genome">
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
22 <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">
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
23 <option value="indexed">Use a built-in genome index</option>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
24 <option value="history">Use a genome from the history and build index</option>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
25 </param>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
26 <when value="indexed">
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
27 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
3
f396b479c2f2 planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit e6a9507eb198c6bf2c63ddae387c262bfc8dbd16
bgruening
parents: 2
diff changeset
28 <options from_data_table="bowtie2_indexes">
0
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
29 <filter type="sort_by" column="2"/>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
30 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
31 </options>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
32 </param>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
33 </when>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
34 <when value="history">
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
35 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
36 <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />-->
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
37 </when>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
38 </conditional>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
39 </xml>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
40 <xml name="re1">
5
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
41 <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"/>
0
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
42 </xml>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
43 <xml name="re2">
4
99dd0efa992b planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
bgruening
parents: 3
diff changeset
44 <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags."
99dd0efa992b planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
bgruening
parents: 3
diff changeset
45 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."/>
0
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
46 </xml>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
47 <xml name="filter_longest_shortest">
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
48 <param argument="--longest" type="text" value="" label="Max insert size" help="Maximum allowable insert size (bps)"/>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
49 <param argument="--shortest" type="text" value="" label="Min insert size" help="Minimum allowable insert size (bps)"/>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
50 </xml>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
51 <xml name="no_fill">
4
99dd0efa992b planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
bgruening
parents: 3
diff changeset
52 <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill"
99dd0efa992b planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
bgruening
parents: 3
diff changeset
53 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"/>
0
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
bgruening
parents:
diff changeset
54 </xml>
5
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
55 <token name="@PAIRED-END_INPUT@"><![CDATA[
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
56 ## Taken from cutadapt except that I don't accept space in name
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
57 #import re
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
58 #set library_type = str($library.type)
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
59 #if $library_type == 'paired':
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
60 #set input_1 = $library.input_1
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
61 #set input_2 = $library.input_2
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
62 #else if $library_type == 'paired_collection'
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
63 #set input_1 = $library.input_1.forward
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
64 #set input_2 = $library.input_1.reverse
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
65 #end if
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
66
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
67 #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
68 #set ext = ".fq.gz"
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
69 #else:
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
70 #set ext = ".fq"
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
71 #end if
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
72 #set read1 = "dataset1" + $ext
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
73 ln -f -s '${input_1}' '$read1' &&
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
74
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
75 #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
76 #set ext2 = ".fq.gz"
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
77 #else:
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
78 #set ext2 = ".fq"
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
79 #end if
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
80 #set read2 = "dataset2" + $ext2
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
81 ln -f -s '${input_2}' '$read2' &&
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
82 ]]>
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
83 </token>
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
84 <xml name="input_paired">
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
85 <conditional name="library">
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
86 <param name="type" type="select" label="How Paired-end reads are organized">
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
87 <option value="paired">Separately</option>
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
88 <option value="paired_collection">Paired-end Collection</option>
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
89 </param>
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
90
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
91 <when value="paired">
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
92 <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;" />
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
93 <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;" />
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
94 </when>
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
95
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
96 <when value="paired_collection">
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
97 <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;" />
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
98 </when>
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
99
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
100 </conditional>
396e8c4ebfee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
bgruening
parents: 4
diff changeset
101 </xml>
1
7f6fa513960e planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b4d9ad47b45abb117a059214e1f7b29d084b4ca3
bgruening
parents: 0
diff changeset
102 </macros>