Mercurial > repos > mvdbeek > bam_readtagger

annotate findcluster.xml @ 81:a446ab055307 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1abb25638cbf5e86c70b59de6453c7c045c2364f"
author mvdbeek
date Sun, 26 Apr 2020 07:59:19 -0400
parents c42dd2551c9c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
79
c42dd2551c9c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit df2b1a906b8772810d995d7887e4e8f04aabc13a"
mvdbeek
parents: 78
diff changeset
1 <tool id="findcluster" name="Find clusters of reads" version="0.5.25">
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
2 <description>in bam files</description>
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
3 <macros>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
4 <import>macros.xml</import>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
5 </macros>
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
6 <requirements>
79
c42dd2551c9c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit df2b1a906b8772810d995d7887e4e8f04aabc13a"
mvdbeek
parents: 78
diff changeset
7 <requirement type="package" version="0.5.25">readtagger</requirement>
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
8 </requirements>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
9 <version_command>findcluster --version</version_command>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
10 <command detect_errors="aggressive"><![CDATA[
34
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents: 33
diff changeset
11 #import re
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents: 33
diff changeset
12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier))
18
8fef53971086 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit f28b0130760f515502b7858bd92adf948a942f39-dirty
mvdbeek
parents: 17
diff changeset
13 ln -f -s $input input.bam &&
17
777fd55e66ac planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit f28b0130760f515502b7858bd92adf948a942f39-dirty
mvdbeek
parents: 16
diff changeset
14 ln -f -s $input.metadata.bam_index input.bam.bai &&
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
15 findcluster
17
777fd55e66ac planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit f28b0130760f515502b7858bd92adf948a942f39-dirty
mvdbeek
parents: 16
diff changeset
16 --input_path input.bam
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
17 #if $transposon_source.ref_file:
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
18 #if str($transposon_source.reference_source_selector) == "history":
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
19 --transposon_reference_fasta '$transposon_source.ref_file'
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
20 #else :
35
02afdbc69591 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e4cd04d8a19b57d6b23da64c3fda8978b51e33ef
mvdbeek
parents: 34
diff changeset
21 --transposon_bwa_index '$transposon_source.ref_file.fields.path'
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
22 #end if
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
23 #end if
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
24 #if $genome_source.ref_file:
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
25 #if str($genome_source.reference_source_selector) == "history":
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
26 --genome_reference_fasta '$genome_source.ref_file'
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
27 #else :
35
02afdbc69591 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e4cd04d8a19b57d6b23da64c3fda8978b51e33ef
mvdbeek
parents: 34
diff changeset
28 --genome_bwa_index '$genome_source.ref_file.fields.path'
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
29 #end if
11
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
30 #end if
40
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
31 #if str($make_bam) == 'True':
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
32 --output_bam '$output_bam'
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
33 #end if
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
34 #if str($make_vcf) == 'True'
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
35 --output_vcf '$output_vcf'
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
36 #end if
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
37 #if str($make_gff) == 'True'
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
38 --output_gff '$output_gff'
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
39 #end if
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
40 #if str($make_fasta) == 'True'
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
41 --output_fasta '$output_fasta'
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
42 #end if
34
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents: 33
diff changeset
43 --sample_name '$sample_name'
8
bf8ffb337cbe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1d14dc7cdb21c782dee08a1d5be1bd956d1a6dc8-dirty
mvdbeek
parents: 7
diff changeset
44 --threads "\${GALAXY_SLOTS:-2}"
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
45 ]]></command>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
46 <inputs>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
47 <param name="input" argument="--input_path" type="data" format="bam"/>
40
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
48 <param name="make_bam" type="boolean" truevalue="True" checked="true" label="Produce an alignment file containing evidence for insertions."/>
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
49 <param name="make_vcf" type="boolean" truevalue="True" checked="true" label="Produce a VCF file describing the insertion that have been found."/>
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
50 <param name="make_gff" type="boolean" truevalue="True" checked="false" label="produce a GFF file describing the insertions that have been found."/>
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
51 <param name="make_fasta" type="boolean" checked="True" truevalue="True" label="Produce a fasta file containing assembled contigs."/>
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
52 <expand macro="reference_source_conditional" reference_type="transposon"/>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
53 <expand macro="reference_source_conditional" reference_type="genome"/>
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
54 </inputs>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
55 <outputs>
40
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
56 <data name="output_bam" format="bam" label="findcluster BAM on $on_string">
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
57 <filter>make_bam</filter>
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
58 </data>
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
59 <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string">
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
60 <filter>make_fasta</filter>
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
61 </data>
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
62 <data name="output_vcf" format="vcf" label="findcluster VCF on $on_string">
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
63 <filter>make_vcf</filter>
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
64 </data>
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
65 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string">
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
66 <filter>make_gff</filter>
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
67 </data>
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
68 </outputs>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
69 <tests>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
70 <test>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
71 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
40
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
72 <param name="make_gff" value="true"/>
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
73 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
40
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
74 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" compare="sim_size"/>
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
75 <output name="output_vcf" file="three_cluster_out.vcf" ftype="vcf" compare="sim_size"/>
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
76 </test>
11
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
77 <test>
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
78 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
79 <param name="transposon_source|reference_source_selector" value="history"/>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
80 <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/>
40
4b1ebfcd0f46 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 38
diff changeset
81 <param name="make_gff" value="true"/>
11
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
82 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
83 <output name="output_gff">
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
84 <assert_contents>
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
85 <has_text text="FBti0019066_rover_Gypsy" />
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
86 </assert_contents>
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
87 </output>
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
88 </test>
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
89 </tests>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
90 <help><![CDATA[
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
91 .. code-block::
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
92
11
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
93 Usage: findcluster [OPTIONS]
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
94
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
95 Find clusters of reads that support a TE insertion.
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
96
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
97 Options:
11
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
98 --input_path PATH Find cluster in this BAM file.
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
99 --region TEXT Find clusters in this Region (Format is
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
100 chrX:2000-1000).
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
101 --max_proper_pair_size INTEGER Maximum proper pairs size. If not given will
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
102 be inferred from the data.
11
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
103 --output_bam PATH Write out BAM file with cluster information
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
104 to this path. Reads will have an additional
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
105 "CD" tag to indicate the cluster number
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
106 --output_gff PATH Write out GFF file with cluster information
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
107 to this path.
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
108 --output_fasta PATH Write out supporting evidence for clusters
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
109 to this path.
11
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
110 --sample_name TEXT Sample name to use when writing out clusters
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
111 in GFF file. Default is to infer the name
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
112 from the input filename.
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
113 --include_duplicates / --no-include_duplicates
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
114 Include reads marked as duplicates when
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
115 finding clusters.
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
116 --transposon_reference_fasta TEXT
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
117 Transposon fasta to align clipped reads to.
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
118 Not necessary if BWA index is provided.
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
119 --transposon_bwa_index TEXT Transposon BWA index to align clipped reads
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
120 to
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
121 --genome_reference_fasta TEXT Genome fasta to align clipped reads to. Not
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
122 necessary if BWA index is provided.
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
123 --genome_bwa_index TEXT Genome BWA index to align clipped reads to
11
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
124 --threads INTEGER RANGE Threads to use for cap3 assembly step
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 30
diff changeset
125 --shm_dir PATH Path to shared memory folder
11
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
126 --version Show the version and exit.
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
127 --help Show this message and exit.
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
128
4
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
129
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
130 ]]></help>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
parents:
diff changeset
131 </tool>