Mercurial > repos > iuc > slamdunk

annotate slamdunk.xml @ 6:f000245e823b 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 0502309b17c070efd9c8ab28e538279055835a45"
author iuc
date Tue, 13 Jul 2021 14:00:42 +0000
parents 40291a9a9c37
children 3af174b9fb79
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
f000245e823b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0502309b17c070efd9c8ab28e538279055835a45"
iuc
parents: 5
diff changeset
1 <tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
0
a4de8b7d6f10 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
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
3 <macros>
9dfecde9fa06 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>
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
5 </macros>
9dfecde9fa06 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
a4de8b7d6f10 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>
a4de8b7d6f10 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
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
9 #import re
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
10
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
11 #if $reference_source.reference_source_selector == 'history':
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
12 ln -f -s '$reference_source.ref_file' reference.fa &&
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
13 #else:
4b677ea9314a 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 &&
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
15 #end if
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
16
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
17 mkdir ./fastq &&
4b677ea9314a 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:
4b677ea9314a 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))
4b677ea9314a 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}' &&
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
21 #end for
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
22
4b677ea9314a 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
17f54c2f4b0c 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
4b677ea9314a 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
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
26 $multimapper.multimap
4b677ea9314a 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:
4b677ea9314a 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
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
29 #end if
4b677ea9314a 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
4b677ea9314a 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
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
32 $advanced.endtoend
4b677ea9314a 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
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
34 -mi $advanced.minID
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
35 -nm=$advanced.maxNM
4b677ea9314a 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
4b677ea9314a 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
4b677ea9314a 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
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
39 -rl $readLength
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
40 -c $covThresh
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
41 ./fastq/*
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
42 ]]></command>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
43 <inputs>
1
9dfecde9fa06 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
4b677ea9314a 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
a4de8b7d6f10 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"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
47 expanded="false">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
48 <section name="filterbed"
a4de8b7d6f10 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">
a4de8b7d6f10 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"
a4de8b7d6f10 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" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
52 </section>
a4de8b7d6f10 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"
a4de8b7d6f10 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"
a4de8b7d6f10 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." />
a4de8b7d6f10 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=""
a4de8b7d6f10 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."
a4de8b7d6f10 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." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
59 </section>
a4de8b7d6f10 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">
a4de8b7d6f10 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"
a4de8b7d6f10 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"
a4de8b7d6f10 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." />
a4de8b7d6f10 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"
a4de8b7d6f10 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"
a4de8b7d6f10 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." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
67 </section>
a4de8b7d6f10 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">
a4de8b7d6f10 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=""
a4de8b7d6f10 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."
a4de8b7d6f10 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" />
a4de8b7d6f10 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"
a4de8b7d6f10 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"
a4de8b7d6f10 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)." />
a4de8b7d6f10 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"
a4de8b7d6f10 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"
a4de8b7d6f10 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)." />
a4de8b7d6f10 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"
a4de8b7d6f10 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"
a4de8b7d6f10 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)." />
a4de8b7d6f10 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"
a4de8b7d6f10 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"
a4de8b7d6f10 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)." />
a4de8b7d6f10 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"
a4de8b7d6f10 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"
a4de8b7d6f10 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)." />
a4de8b7d6f10 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"
a4de8b7d6f10 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"
a4de8b7d6f10 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)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
90 </section>
a4de8b7d6f10 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"
a4de8b7d6f10 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"
a4de8b7d6f10 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)." />
a4de8b7d6f10 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"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
95 label="Read length"
a4de8b7d6f10 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)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
97 </inputs>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
98 <outputs>
2
4b677ea9314a 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 ${on_string}: BAM">
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
100 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bam$" format="bam" directory="./out/filter" visible="false" />
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
101 </collection>
4b677ea9314a 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 ${on_string}: Count TSV">
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
103 <discover_datasets pattern="(?P&lt;name&gt;.+)_tcount.tsv$" format="tabular" directory="./out/count" visible="false" />
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
104 </collection>
4b677ea9314a 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 ${on_string}: VCF">
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
106 <discover_datasets pattern="(?P&lt;name&gt;.+)_snp.vcf$" format="vcf" directory="./out/snp" visible="false" />
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
107 </collection>
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
108 </outputs>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
109 <tests>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
110 <test>
1
9dfecde9fa06 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
a4de8b7d6f10 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" />
a4de8b7d6f10 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" />
a4de8b7d6f10 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
4b677ea9314a 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
a4de8b7d6f10 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" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
117 <section name="quantseq">
a4de8b7d6f10 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" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
119 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
120 <section name="advanced">
a4de8b7d6f10 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" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
122 </section>
2
4b677ea9314a 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">
4b677ea9314a 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" />
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
125 </output_collection>
4b677ea9314a 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">
4b677ea9314a 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"
5
40291a9a9c37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 64bbe6ec9a3f3cd6241fa4cf0e0548e0e67629a0"
iuc
parents: 3
diff changeset
128 compare="re_match" />
2
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
129 </output_collection>
4b677ea9314a 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">
4b677ea9314a 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" />
4b677ea9314a 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
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
133 </test>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
134 <test>
1
9dfecde9fa06 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
a4de8b7d6f10 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" />
5
40291a9a9c37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 64bbe6ec9a3f3cd6241fa4cf0e0548e0e67629a0"
iuc
parents: 3
diff changeset
137 <param name="ref_file" value="hg38full" />
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
138 <param name="Reference" value="actb.bed" />
2
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
139 <param name="reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
140 <param name="readLength" value="100" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
141 <section name="quantseq">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
142 <param name="trim5" value="0" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
143 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
144 <section name="advanced">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
145 <param name="minBaseQual" value="27" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
146 </section>
2
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
147 <output_collection name="outputBam">
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
148 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" />
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
149 </output_collection>
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
150 <output_collection name="outputTsv">
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
151 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
5
40291a9a9c37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 64bbe6ec9a3f3cd6241fa4cf0e0548e0e67629a0"
iuc
parents: 3
diff changeset
152 compare="re_match" />
2
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
153 </output_collection>
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
154 <output_collection name="outputVcf">
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
155 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
iuc
parents: 1
diff changeset
156 </output_collection>
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
157 </test>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
158 </tests>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
159 <help><![CDATA[
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
160 SLAM-seq
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
161 ========
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
162
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
163 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.
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
164
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
165 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>`_
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
166
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
167 Slamdunk
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
168 ========
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
169
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
170 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.
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
171
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
172 =============== ==========================================================================================================================================================
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
173 Parameter Description
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
174 =============== ==========================================================================================================================================================
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
175 **Genome** The reference fasta file (Genome assembly).
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
176 **Reference** BED-file containing coordinates for 3' UTRs.
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
177 **Reads** Sample FASTQ(gz) files.
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
178 **Read length** Maximum length of reads (usually 50, 100, 150).
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
179 =============== ==========================================================================================================================================================
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
180
1
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
181 This will run the entire *slamdunk* analysis (`slamdunk all`) with the most relevant output files being:
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
182
1
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
183 * Tab-separated *tcount* file (Count TSV) containing the SLAM-seq statistics per UTR
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
184 * BAM-file with the final filtered mapped reads
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
185 * VCF file of variants called on the final filtered alignments
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
186
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
187 These files can be input to the **Alleyoop** tool for visualization and further processing. See the `Slamdunk documentation`_ for more information.
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
188
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
189 ------------------------------------------------------
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
190
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
191 Multimapper recovery
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
192 --------------------
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
193
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
194 To utilize multimapper recovery, modify the following parameters. You must either choose a separate 3' UTR file or activate filtering
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
195 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.
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
196
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
197 =================================================== =========================================================
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
198 Parameter Description
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
199 =================================================== =========================================================
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
200 **Maximum number of alignments to report per read** The maximum number of multimapper alignments to consider.
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
201 **Use separate 3' UTR bed to filter multimappers.** 3' UTR bed file to filter.
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
202 **Use reference bed file to resolve multimappers.** Use reference as 3' UTR bed file to filter.
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
203 =================================================== =========================================================
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
204
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
205 ------------------------------------------------------
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
206
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
207 T>C conversions
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
208 ---------------
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
209
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
210 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>`_
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
211
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
212 This can be controlled by the following parameter:
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
213
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
214 ============================ ================================================================================
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
215 Parameter Description
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
216 ============================ ================================================================================
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
217 **T>C conversion threshold** Minimum number of T>C conversions to consider a read as T>C read.
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
218 ============================ ================================================================================
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
219
1
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
220 .. _`Slamdunk documentation`: http://t-neumann.github.io/slamdunk/docs.html
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
221
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
222 ]]></help>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
223 <citations>
1
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents: 0
diff changeset
224 <expand macro="citations" />
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
225 </citations>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
parents:
diff changeset
226 </tool>