Mercurial > repos > bgruening > hicup2juicer

annotate hicup2juicer.xml @ 0:396bdc215399 draft

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 50173a1994a72d9774fd46777de94dd02d35bd42
author bgruening
date Mon, 24 Oct 2022 15:58:52 +0000
parents
children 82641e9a86cb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
1 <tool id="hicup2juicer" name="Hicup to juicer converter" version="@VERSION@+galaxy0">
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
2 <description></description>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
3 <macros>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
4 <import>hicup_macros.xml</import>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
5 </macros>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
6 <expand macro="requirements_hicup" />
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
8 #if $input_file.ext != 'sam':
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
9 #set ext='bam'
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
10 #else:
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
11 #set ext='sam'
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
12 #end if
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
13 ln -s '$input_file' input.$ext &&
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
14 hicup2juicer input.$ext
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
15 ]]>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
16 </command>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
17 <inputs>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
18 <param name="input_file" type="data" format="qname_sorted.bam,sam" label="Output of HiCUP to convert" />
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
19 </inputs>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
20 <outputs>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
21 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Pairs in juicebox format" from_work_dir="*.prejuicer" />
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
22 </outputs>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
23 <tests>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
24 <test expect_num_outputs="1">
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
25 <param name="input_file" value="dataset1_2.hicup.bam"/>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
26 <output name="output" value="dataset1_2.hicup.bam.prejuicer"/>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
27 </test>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
28 </tests>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
29 <help><![CDATA[
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
30
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
31 HiCUP homepage: www.bioinformatics.babraham.ac.uk/projects/hicup
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
32
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
33 The hicup2juicer script converts HiCUP BAM/SAM files to a format compatible
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
34 with Juicer and JuiceBox( https://github.com/aidenlab/juicer ).
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
35 Outputfiles generated by this script may be converted to Juicer ".hic" files
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
36 using the "pre" command as described at: https://github.com/aidenlab/juicer/wiki/Pre
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
37
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
38 The script does not use restriction site coordinates when generating output.
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
39
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
40 FUNCTION
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
41
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
42 HiCUP generates SAM/BAM files of mapped, filtered paired-end reads
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
43 constituting the sequenced valid Hi-C di-tags. These may then be analysed by a
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
44 variety of specialised tools, but before this is possible the datasets will
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
45 need parsing into an appropriate format.
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
46
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
47 The hicup2juicer script converts HiCUP BAM/SAM files to a tab-delimited format
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
48 comprising 7 columns, with read pairs on the same line:
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
49
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
50 <readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
51 str = strand (0 for forward, anything else for reverse)
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
52 chr = chromosome (must be a chromosome in the genome)
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
53 pos = position
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
54 frag = restriction site fragment
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
55 mapq = mapping quality score
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
56
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
57 Column1: Readpair index number (starting at 1)
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
58 Column2: forward read strand (0 = positive strand, 1 = negative strand)
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
59 Column3: forward read chromosome name
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
60 Column4: forward read position
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
61 Column5: forward read fragment id (set to the dummy value 0)
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
62 Column6: reverse read strand (0 = positive strand, 1 = negative strand)
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
63 Column7: reverse read chromosome name
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
64 Column8: reverse read position
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
65 Column9: reverse read fragment id (set to the dummy value 1)
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
66 Column10: forward read MAPQ score
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
67 Column11: reverse read MAPQ score
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
68
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
69
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
70 COMMAND LINE OPTIONS
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
71
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
72 --help Print help message and exit
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
73 --version Print the program version and exit
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
74 --zip Write output to a gzip file
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
75
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
76 Full instructions on running the pipeline can be found at:
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
77 www.bioinformatics.babraham.ac.uk/projects/hicup
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
78
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
79 Steven Wingett, Babraham Institute, Cambridge, UK
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
80 ]]>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
81 </help>
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
82 <expand macro="citation_hicup" />
396bdc215399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
bgruening
parents:
diff changeset
83 </tool>