Mercurial > repos > iuc > bctools_extract_crosslinked_nucleotides

annotate coords2clnt.xml @ 4:12a5e6fa850e 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/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a6a6774ae353f915a5ca34af8f281edd91e5c665
author iuc
date Fri, 04 Oct 2024 08:57:18 +0000
parents 91f27e8a2535
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
12a5e6fa850e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a6a6774ae353f915a5ca34af8f281edd91e5c665
iuc
parents: 2
diff changeset
1 <tool id="bctools_extract_crosslinked_nucleotides" name="Get crosslinked nucleotides" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
2 <description>from full alignments</description>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
3 <macros>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
4 <import>macros.xml</import>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
5 </macros>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
8 coords2clnt.py
2
91f27e8a2535 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 513a54a013c5762aa6099fe044b2d3acf4a76881
iuc
parents: 0
diff changeset
9 $threeprime
0
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
10 '$alignment_coordinates'
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
11 > '$crosslinking_coordinates'
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
12 ]]></command>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
13 <inputs>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
14 <param name="alignment_coordinates" type="data" format="bed" label="Alignments in BED format"/>
2
91f27e8a2535 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 513a54a013c5762aa6099fe044b2d3acf4a76881
iuc
parents: 0
diff changeset
15 <param argument="--threeprime" type="boolean" truevalue="--threeprime" falsevalue="" checked="false"
91f27e8a2535 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 513a54a013c5762aa6099fe044b2d3acf4a76881
iuc
parents: 0
diff changeset
16 label="Set position one nt downstream of 3'-end as crosslinked nucleotide"
91f27e8a2535 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 513a54a013c5762aa6099fe044b2d3acf4a76881
iuc
parents: 0
diff changeset
17 help="Set position one nt downstream of 3'-end as crosslinked nucleotide. By default the crosslink site will be assumed to be one nt upstream of the 5'-end of the read."/>
0
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
18 </inputs>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
19 <outputs>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
20 <data name="crosslinking_coordinates" format="bed"/>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
21 </outputs>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
22 <tests>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
23 <test>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
24 <param name="alignment_coordinates" value="merged_pcr_dupes.bed"/>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
25 <output name="crosslinking_coordinates" file="merged_pcr_dupes_clnts.bed"/>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
26 </test>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
27 </tests>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
28 <help><![CDATA[
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
29
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
30 bctools - Get crosslinked nucleotides from full alignments
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
31 ==========================================================
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
32
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
33 Given coordinates of aligned reads in BED format, calculate positions of the
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
34 crosslinked nucleotides. Crosslinked nts are assumed to be one nt upstream of
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
35 the 5'-end of the read.
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
36
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
37 Input
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
38 -----
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
39
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
40 * six column BED file containing coordinates of aligned reads
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
41
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
42 Output
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
43 ------
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
44
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
45 * six column BED file containing coordinates of crosslinking events
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
46
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
47 ]]></help>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
48 <expand macro="citations"/>
66d1f96c5600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
iuc
parents:
diff changeset
49 </tool>