Mercurial > repos > mvdbeek > bam_readtagger

annotate findcluster.xml @ 40:bb09f4ee2ff8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8e9ede772dcffc699ffd4bf0cfd83abae29b0a01-dirty
author mvdbeek
date Sat, 06 Jan 2018 07:21:07 -0500
parents 7cad80dc3b58
children 29734dbad6de
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
40
bb09f4ee2ff8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8e9ede772dcffc699ffd4bf0cfd83abae29b0a01-dirty
mvdbeek
parents: 39
diff changeset
1 <tool id="findcluster" name="Find clusters of reads" version="0.4.6">
5
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
2 <description>in bam files</description>
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
3 <macros>
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
4 <import>macros.xml</import>
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
5 </macros>
5
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
6 <requirements>
40
bb09f4ee2ff8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8e9ede772dcffc699ffd4bf0cfd83abae29b0a01-dirty
mvdbeek
parents: 39
diff changeset
7 <requirement type="package" version="0.4.6">readtagger</requirement>
5
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
8 </requirements>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
9 <version_command>findcluster --version</version_command>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
10 <command detect_errors="aggressive"><![CDATA[
37
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents: 36
diff changeset
11 #import re
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents: 36
diff changeset
12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier))
20
44bbb5c4553f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e3effe4ab3ded37fb610f53deb4d0082daf7fdac
mvdbeek
parents: 19
diff changeset
13 ln -f -s $input input.bam &&
44bbb5c4553f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e3effe4ab3ded37fb610f53deb4d0082daf7fdac
mvdbeek
parents: 19
diff changeset
14 ln -f -s $input.metadata.bam_index input.bam.bai &&
5
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
15 findcluster
20
44bbb5c4553f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e3effe4ab3ded37fb610f53deb4d0082daf7fdac
mvdbeek
parents: 19
diff changeset
16 --input_path input.bam
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
17 #if $transposon_source.ref_file:
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
18 #if str($transposon_source.reference_source_selector) == "history":
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
19 --transposon_reference_fasta '$transposon_source.ref_file'
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
20 #else :
38
700df574a69c planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e4cd04d8a19b57d6b23da64c3fda8978b51e33ef
mvdbeek
parents: 37
diff changeset
21 --transposon_bwa_index '$transposon_source.ref_file.fields.path'
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
22 #end if
32
5dcad82862b4 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 3cb122f0ab5dc2ad7bb61d1abdd13865142e25b8-dirty
mvdbeek
parents: 31
diff changeset
23 #end if
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
24 #if $genome_source.ref_file:
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
25 #if str($genome_source.reference_source_selector) == "history":
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
26 --genome_reference_fasta '$genome_source.ref_file'
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
27 #else :
38
700df574a69c planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e4cd04d8a19b57d6b23da64c3fda8978b51e33ef
mvdbeek
parents: 37
diff changeset
28 --genome_bwa_index '$genome_source.ref_file.fields.path'
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
29 #end if
12
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
30 #end if
5
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
31 --output_bam '$output_bam'
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
32 --output_gff '$output_gff'
20
44bbb5c4553f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e3effe4ab3ded37fb610f53deb4d0082daf7fdac
mvdbeek
parents: 19
diff changeset
33 --output_fasta '$output_fasta'
37
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents: 36
diff changeset
34 --sample_name '$sample_name'
9
04e14e0da336 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1d14dc7cdb21c782dee08a1d5be1bd956d1a6dc8
mvdbeek
parents: 8
diff changeset
35 --threads "\${GALAXY_SLOTS:-2}"
5
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
36 ]]></command>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
37 <inputs>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
38 <param name="input" argument="--input_path" type="data" format="bam"/>
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
39
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
40 <expand macro="reference_source_conditional" reference_type="transposon"/>
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
41 <expand macro="reference_source_conditional" reference_type="genome"/>
5
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
42 </inputs>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
43 <outputs>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
44 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
20
44bbb5c4553f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e3effe4ab3ded37fb610f53deb4d0082daf7fdac
mvdbeek
parents: 19
diff changeset
45 <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"/>
5
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
46 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
47 </outputs>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
48 <tests>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
49 <test>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
50 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
51 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
52 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
53 </test>
12
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
54 <test>
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
55 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
56 <param name="transposon_source|reference_source_selector" value="history"/>
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
57 <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/>
12
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
58 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
59 <output name="output_gff">
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
60 <assert_contents>
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
61 <has_text text="FBti0019066_rover_Gypsy" />
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
62 </assert_contents>
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
63 </output>
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
64 </test>
5
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
65 </tests>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
66 <help><![CDATA[
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
67 .. code-block::
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
68
12
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
69 Usage: findcluster [OPTIONS]
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
70
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
71 Find clusters of reads that support a TE insertion.
5
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
72
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
73 Options:
12
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
74 --input_path PATH Find cluster in this BAM file.
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
75 --region TEXT Find clusters in this Region (Format is
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
76 chrX:2000-1000).
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
77 --max_proper_pair_size INTEGER Maximum proper pairs size. If not given will
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
78 be inferred from the data.
12
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
79 --output_bam PATH Write out BAM file with cluster information
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
80 to this path. Reads will have an additional
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
81 "CD" tag to indicate the cluster number
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
82 --output_gff PATH Write out GFF file with cluster information
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
83 to this path.
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
84 --output_fasta PATH Write out supporting evidence for clusters
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
85 to this path.
12
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
86 --sample_name TEXT Sample name to use when writing out clusters
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
87 in GFF file. Default is to infer the name
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
88 from the input filename.
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
89 --include_duplicates / --no-include_duplicates
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
90 Include reads marked as duplicates when
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
91 finding clusters.
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
92 --transposon_reference_fasta TEXT
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
93 Transposon fasta to align clipped reads to.
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
94 Not necessary if BWA index is provided.
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
95 --transposon_bwa_index TEXT Transposon BWA index to align clipped reads
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
96 to
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
97 --genome_reference_fasta TEXT Genome fasta to align clipped reads to. Not
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
98 necessary if BWA index is provided.
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
99 --genome_bwa_index TEXT Genome BWA index to align clipped reads to
12
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
100 --threads INTEGER RANGE Threads to use for cap3 assembly step
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 32
diff changeset
101 --shm_dir PATH Path to shared memory folder
12
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
102 --version Show the version and exit.
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
103 --help Show this message and exit.
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
104
5
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
105
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
106 ]]></help>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
parents:
diff changeset
107 </tool>