Mercurial > repos > iuc > slamdunk

annotate slamdunk.xml @ 4:fe3fe68b09a7 draft

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/slamdunk commit ea4590f61d7764eb431986c16785e599191615a6
author iuc
date Fri, 24 May 2019 13:30:30 -0400
parents 24657d5edede
children 8b62f89924a7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
1 <tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy2">
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
2 <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description>
1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
3 <macros>
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
4 <import>macros.xml</import>
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
5 </macros>
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
6 <expand macro="requirements" />
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
7 <version_command>slamdunk --version</version_command>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
2
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
9 #import re
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
10
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
11 #if $reference_source.reference_source_selector == 'history':
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
12 ln -f -s '$reference_source.ref_file' reference.fa &&
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
13 #else:
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
14 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
15 #end if
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
16
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
17 mkdir ./fastq &&
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
18 #for $fastq in $reads:
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
19 #set $fastq_name = re.sub('[^\w\-\.]', '_', str($fastq.element_identifier))
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
20 ln -s '$fastq' './fastq/${fastq_name}' &&
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
21 #end for
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
22
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
23 slamdunk all -r reference.fa -b '$Reference' -o ./out
3
24657d5edede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 11770937d250d7a332875becf06b9a42b17c46d1
iuc
parents: 2
diff changeset
24 -t \${GALAXY_SLOTS:-1}
2
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
25 -n $multimapper.multimappers
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
26 $multimapper.multimap
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
27 #if $multimapper.filterbed.bedtofilter:
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
28 -fb $multimapper.filterbed.bedtofilter
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
29 #end if
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
30 -5 $quantseq.trim5
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
31 -a $quantseq.maxpolyA
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
32 $advanced.endtoend
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
33 -mq $advanced.minMQ
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
34 -mi $advanced.minID
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
35 -nm=$advanced.maxNM
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
36 -mc $advanced.minCov
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
37 -mv $advanced.minVar
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
38 -mbq $advanced.minBaseQual
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
39 -rl $readLength
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
40 -c $covThresh
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
41 ./fastq/*
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
42 ]]></command>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
43 <inputs>
1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
44 <expand macro="reference_files" />
2
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
45 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" multiple="True" label="FASTQ files"/>
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
46 <section name="multimapper" title="Multimapper recovery"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
47 expanded="false">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
48 <section name="filterbed"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
49 title="Use separate 3' UTR bed to filter multimappers." expanded="false">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
50 <param name="bedtofilter" type="data" format="bed" optional="true"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
51 label="Bed to filter" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
52 </section>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
53 <param name="multimappers" type="integer" min="1" value="1"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
54 label="Maximum number of alignments to report per read"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
55 help="The maximum number of alignments is used to track multimapping read alignments. The more are allowed, the more sensitive the multimapper filtering will be, but also the longer the runtime will be. 100 was used in previous publications." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
56 <param name="multimap" type="boolean" truevalue="--multimap" falsevalue=""
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
57 label="Use reference bed file to resolve multimappers."
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
58 help="Enable multimapper recovery, requires -n to be set to a value > 1 to have impact." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
59 </section>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
60 <section name="quantseq" title="Quantseq" expanded="false">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
61 <param name="trim5" type="integer" min="0" value="12"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
62 label="Number of bp to remove from the 5' end of all reads"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
63 help="For Lexogen's Quantseq kit and previous SLAM-seq papers a clipping of 12 bp from the 5' end is recommended." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
64 <param name="maxpolyA" type="integer" min="0" value="4"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
65 label="Maximum number of As at the 3' end of a read"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
66 help="The maximum number of allowed As at the 3' end of a read. All A-stretches that exceed this threshold are clipped because they are likely part of the poly-A tail." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
67 </section>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
68 <section name="advanced" title="Advanced settings." expanded="false">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
69 <param name="endtoend" type="boolean" truevalue="--endtoend" falsevalue=""
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
70 label="Enable end-to-end alignments for mapping."
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
71 help="Enable end-to-end alignments for mapping in slamdunk with --endtoend" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
72 <param name="minMQ" type="integer" min="0" value="2"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
73 label="Minimum mapping quality"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
74 help="Minimum mapping quality to consider alignments (default: 2)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
75 <param name="minID" type="float" min="0" value="0.95"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
76 label="Minimum alignment identity"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
77 help="Minimum alignment-identity to consider alignments (default: 0.95)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
78 <param name="maxNM" type="integer" value="-1"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
79 label="Maximum number of mismatches"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
80 help="Maximum number of mismatches to consider alignments. Negative numbers deactivate filter (default: -1)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
81 <param name="minCov" type="integer" min="0" value="10"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
82 label="Minimum coverage to call variant"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
83 help="Minimum coverage to call variant (default: 10)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
84 <param name="minVar" type="float" min="0" value="0.8"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
85 label="Minimum variant fraction to call variant"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
86 help="Minimum variant fraction to call variant (default: 0.8)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
87 <param name="minBaseQual" type="integer" min="0" value="27"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
88 label="Minimum base quality"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
89 help="Minimum base quality for T>C conversions (default: 27)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
90 </section>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
91 <param name="covThresh" type="integer" min="1" value="1"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
92 label="T>C conversion threshold"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
93 help="Number of T>C conversions required to count a read as a T>C read (default: 1)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
94 <param name="readLength" type="integer" min="50" value="50"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
95 label="Read length"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
96 help="Maximum read length (before trimming)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
97 </inputs>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
98 <outputs>
2
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
99 <collection name="outputBam" type="list" label="${tool.name} on ${on_string}: BAM">
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
100 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bam$" format="bam" directory="./out/filter" visible="false" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
101 </collection>
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
102 <collection name="outputTsv" type="list" label="${tool.name} on ${on_string}: Count TSV">
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
103 <discover_datasets pattern="(?P&lt;name&gt;.+)_tcount.tsv$" format="tabular" directory="./out/count" visible="false" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
104 </collection>
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
105 <collection name="outputVcf" type="list" label="${tool.name} on ${on_string}: VCF">
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
106 <discover_datasets pattern="(?P&lt;name&gt;.+)_snp.vcf$" format="vcf" directory="./out/snp" visible="false" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
107 </collection>
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
108 </outputs>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
109 <tests>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
110 <test>
1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
111 <!--Ensure default outputs work -->
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
112 <param name="reference_source_selector" value="history" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
113 <param name="ref_file" value="ref.fa" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
114 <param name="Reference" value="actb.bed" />
2
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
115 <param name="reads" value="reads.fq" />
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
116 <param name="readLength" value="100" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
117 <section name="quantseq">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
118 <param name="trim5" value="0" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
119 </section>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
120 <section name="advanced">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
121 <param name="minBaseQual" value="27" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
122 </section>
2
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
123 <output_collection name="outputBam">
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
124 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
125 </output_collection>
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
126 <output_collection name="outputTsv">
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
127 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
128 lines_diff="2" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
129 </output_collection>
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
130 <output_collection name="outputVcf">
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
131 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
132 </output_collection>
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
133 </test>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
134 <test>
1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
135 <!--Ensure built-in fasta works -->
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
136 <param name="reference_source_selector" value="cached" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
137 <param name="Reference" value="actb.bed" />
2
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
138 <param name="reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
139 <param name="readLength" value="100" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
140 <section name="quantseq">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
141 <param name="trim5" value="0" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
142 </section>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
143 <section name="advanced">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
144 <param name="minBaseQual" value="27" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
145 </section>
2
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
146 <output_collection name="outputBam">
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
147 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
148 </output_collection>
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
149 <output_collection name="outputTsv">
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
150 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
151 lines_diff="2" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
152 </output_collection>
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
153 <output_collection name="outputVcf">
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
154 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
155 </output_collection>
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
156 </test>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
157 </tests>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
158 <help><![CDATA[
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
159 SLAM-seq
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
160 ========
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
161
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
162 SLAM-seq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. When combined with metabolic labeling protocols, SLAM-seq allows to study the intracellular RNA dynamics, from transcription, RNA processing to RNA stability.
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
163
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
164 Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 <https://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4435.html>`_
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
165
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
166 Slamdunk
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
167 ========
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
168
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
169 To analyze a given SLAM-seq dataset with *slamdunk* without recovering multimappers, you only need to provide the following files and keep everything else to the default parameters.
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
170
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
171 =============== ==========================================================================================================================================================
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
172 Parameter Description
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
173 =============== ==========================================================================================================================================================
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
174 **Genome** The reference fasta file (Genome assembly).
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
175 **Reference** BED-file containing coordinates for 3' UTRs.
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
176 **Reads** Sample FASTQ(gz) files.
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
177 **Read length** Maximum length of reads (usually 50, 100, 150).
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
178 =============== ==========================================================================================================================================================
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
179
1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
180 This will run the entire *slamdunk* analysis (`slamdunk all`) with the most relevant output files being:
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
181
1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
182 * Tab-separated *tcount* file (Count TSV) containing the SLAM-seq statistics per UTR
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
183 * BAM-file with the final filtered mapped reads
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
184 * VCF file of variants called on the final filtered alignments
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
185
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
186 These files can be input to the **Alleyoop** tool for visualization and further processing. See the `Slamdunk documentation`_ for more information.
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
187
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
188 ------------------------------------------------------
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
189
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
190 Multimapper recovery
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
191 --------------------
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
192
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
193 To utilize multimapper recovery, modify the following parameters. You must either choose a separate 3' UTR file or activate filtering
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
194 on the supplied reference file. Will only yield different results than a unique-mapping run by specifying a number > 1 as maximum number of multimapper aligments to consider.
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
195
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
196 =================================================== =========================================================
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
197 Parameter Description
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
198 =================================================== =========================================================
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
199 **Maximum number of alignments to report per read** The maximum number of multimapper alignments to consider.
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
200 **Use separate 3' UTR bed to filter multimappers.** 3' UTR bed file to filter.
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
201 **Use reference bed file to resolve multimappers.** Use reference as 3' UTR bed file to filter.
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
202 =================================================== =========================================================
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
203
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
204 ------------------------------------------------------
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
205
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
206 T>C conversions
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
207 ---------------
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
208
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
209 Depending on the use case, more stringent or more lenient measures of T>C conversion and T>C reads are required such as 2 T>C by `Muhar et al., Science, 2018; http://doi.org/10.1126/science.aao2793 <http://science.sciencemag.org/content/early/2018/04/04/science.aao2793>`_
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
210
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
211 This can be controlled by the following parameter:
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
212
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
213 ============================ ================================================================================
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
214 Parameter Description
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
215 ============================ ================================================================================
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
216 **T>C conversion threshold** Minimum number of T>C conversions to consider a read as T>C read.
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
217 ============================ ================================================================================
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
218
1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
219 .. _`Slamdunk documentation`: http://t-neumann.github.io/slamdunk/docs.html
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
220
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
221 ]]></help>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
222 <citations>
1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
223 <expand macro="citations" />
0
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
224 </citations>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
225 </tool>