annotate artbio_bam_cleaning.xml @ 10:ba3e6a71acb8 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 4a36bccf4c745cc7f1f13189140252721ff5e61d"
author artbio
date Fri, 31 Dec 2021 00:04:07 +0000
parents cb94e94e0f4e
children 6815060fb056
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
ba3e6a71acb8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 4a36bccf4c745cc7f1f13189140252721ff5e61d"
artbio
parents: 9
diff changeset
1 <tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy3">
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
2 <description>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
3 on flags and PCR Duplicates and MD recalibration
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
4 </description>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
5 <macros>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
6 <import>macro.xml</import>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
7 </macros>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
8 <requirements>
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
9 <requirement type="package" version="1.6=hb116620_7">samtools</requirement>
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
10 <requirement type="package" version="0.8.1=h41abebc_0">sambamba</requirement>
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
11 <requirement type="package" version="1.3.5=py39hba5d119_3">freebayes</requirement>
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
12 </requirements>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
13 <stdio>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
14 <exit_code range="1:" level="fatal" description="Error occured" />
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
15 </stdio>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
16 <command detect_errors="exit_code"><![CDATA[
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
17 @pipefail@
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
18 @set_fasta_index@
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
19 #set input_base = 'input'
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
20 ln -f -s $input_bam.metadata.bam_index input.bam.bai &&
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
21 ln -s $input_bam input.bam &&
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
22 sambamba view -h -t \${GALAXY_SLOTS:-2} --filter="mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped) and not(duplicate)" -f "bam" ${input_base}".bam"
4
15ada8e1580a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 13e2d0837000c2557f9590aa861a9fd5bc16cbcc"
artbio
parents: 3
diff changeset
23 | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
5
ebdaf5b3d6a7 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b846085c8b8e29bb067a3cdcb90355117aeebf42"
artbio
parents: 4
diff changeset
24 | samtools calmd -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa
8
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
25 #if $specify_outputs == 'just_calMD':
6
999c2b871f36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 587b99e907726b20f0cdd978be8f9ed257a68243"
artbio
parents: 5
diff changeset
26 > $calmd
10
ba3e6a71acb8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 4a36bccf4c745cc7f1f13189140252721ff5e61d"
artbio
parents: 9
diff changeset
27 #else if $specify_outputs == 'both':
6
999c2b871f36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 587b99e907726b20f0cdd978be8f9ed257a68243"
artbio
parents: 5
diff changeset
28 | tee $calmd
999c2b871f36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 587b99e907726b20f0cdd978be8f9ed257a68243"
artbio
parents: 5
diff changeset
29 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
9
cb94e94e0f4e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit ed02ebb9addd947f34d9491420bc325e941eb468"
artbio
parents: 8
diff changeset
30 #else:
cb94e94e0f4e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit ed02ebb9addd947f34d9491420bc325e941eb468"
artbio
parents: 8
diff changeset
31 | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
6
999c2b871f36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 587b99e907726b20f0cdd978be8f9ed257a68243"
artbio
parents: 5
diff changeset
32 #end if
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
33 ]]></command>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
34 <inputs>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
35 <expand macro="reference_source_conditional" />
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
36 <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>
8
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
37 <param name="specify_outputs" type="select" label="specify cleaned output(s)"
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
38 display="radio"
8
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
39 help="The tool first generates MD-recalibrated alignements, then discards
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
40 aberrant Mapping Quality alignements generated by calMD recalibration.
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
41 One, the other, or both types of outputs can be retained by the tool">
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
42 <option value="just_calMD">Alignments are only MD-recalibrated (for split or discordant read aware variant callers)</option>
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
43 <option value="calMDandMQ" selected="true">Alignments are MD-recalibrated AND mapping quality &gt; 254 are discarded (for snv and small indel callers)</option>
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
44 <option value="both">Both types of outputs are retained</option>
6
999c2b871f36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 587b99e907726b20f0cdd978be8f9ed257a68243"
artbio
parents: 5
diff changeset
45 </param>
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
46 </inputs>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
47 <outputs>
8
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
48 <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)">
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
49 <filter>specify_outputs == 'just_calMD' or specify_outputs == 'both'</filter>
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
50 </data>
6
999c2b871f36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 587b99e907726b20f0cdd978be8f9ed257a68243"
artbio
parents: 5
diff changeset
51 <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)">
8
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
52 <filter>specify_outputs == 'calMDandMQ' or specify_outputs == 'both'</filter>
6
999c2b871f36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 587b99e907726b20f0cdd978be8f9ed257a68243"
artbio
parents: 5
diff changeset
53 </data>
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
54 </outputs>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
55 <tests>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
56 <test>
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
57 <param name="input_bam" value="chr22_sample.bam" ftype="bam" />
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
58 <param name="reference_source_selector" value="history" />
8
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
59 <param name="specify_outputs" value="calMDandMQ" />
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
60 <param name="ref_file" value="chr22.fa" />
8
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
61 <output name="fullfilter" file="full.bam" ftype="bam" />
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
62 </test>
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
63 <test>
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
64 <param name="input_bam" value="chr22_sample.bam" ftype="bam" />
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
65 <param name="reference_source_selector" value="history" />
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
66 <param name="ref_file" value="chr22.fa" />
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
67 <param name="specify_outputs" value="both" />
4
15ada8e1580a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 13e2d0837000c2557f9590aa861a9fd5bc16cbcc"
artbio
parents: 3
diff changeset
68 <output name="calmd" file="calmd.bam" ftype="bam" />
15ada8e1580a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 13e2d0837000c2557f9590aa861a9fd5bc16cbcc"
artbio
parents: 3
diff changeset
69 <output name="fullfilter" file="full.bam" ftype="bam" />
15ada8e1580a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 13e2d0837000c2557f9590aa861a9fd5bc16cbcc"
artbio
parents: 3
diff changeset
70 </test>
15ada8e1580a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 13e2d0837000c2557f9590aa861a9fd5bc16cbcc"
artbio
parents: 3
diff changeset
71 <test>
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
72 <param name="input_bam" value="chr22_sample.bam" ftype="bam" />
4
15ada8e1580a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 13e2d0837000c2557f9590aa861a9fd5bc16cbcc"
artbio
parents: 3
diff changeset
73 <param name="reference_source_selector" value="history" />
8
b12e50bcddd2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
artbio
parents: 7
diff changeset
74 <param name="specify_outputs" value="just_calMD" />
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
75 <param name="ref_file" value="chr22.fa" />
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
76 <output name="calmd" file="calmd.bam" ftype="bam" />
1
b550841f568b "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 2d441fd84bf17c0899d0b57ea35c84cb83b77119"
artbio
parents: 0
diff changeset
77 </test>
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
78 </tests>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
79 <help>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
80 ARTbio bam cleaning overview
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
81 ============================
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
82
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
83 .. class:: infomark
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
84
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
85 This tool is wrapping several cleaning steps to produce bam files suitable for subsequent
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
86 analyses with lumpy-smoove (or other large structural variation callers) or with
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
87 somatic-varscan (or other small structural variation callers)
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
88
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
89
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
90 Workflow
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
91 =============
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
92
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
93 .. class:: infomark
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
94
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
95 The tool is using the following command line for filtering:
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
96
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
97 ::
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
98
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
99 sambamba view -h -t 8 --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped) and not(duplicate)' -f 'bam' $input_base".bam"
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
100 &#124; bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
101 &#124; samtools calmd -C 50 -b -@ 4 - reference.fa &gt; $input_base".filt1.dedup.bamleft.calmd.bam" ;
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
102 sambamba view -h -t 8 --filter='mapping_quality &lt;&#61; 254' -f 'bam' -o $input_base".filt1.dedup.bamleft.calmd.filt2.bam" $input_base".filt1.dedup.bamleft.calmd.bam"
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
103
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
104 .. class:: warningmark
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
105
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
106 From version **1.7+galaxy0**, this tool assumes that the input bam already has its
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
107 optical/PCR duplicate alignments marked appropriately in their flag value. If it is not the
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
108 case, it may be necessary to use tool that perform this job, for instance samtools markdup,
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
109 or sambamba markdup.
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents: 6
diff changeset
110
0
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
111 Purpose
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
112 --------
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
113
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
114 This "workflow" tool was generated in order to limit the number of ``python metadata/set.py`` jobs
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
115 which occur at each step of standard galaxy workflows. Indeed, these jobs are poorly optimized and may last considerable
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
116 amounts of time when datasets are large, at each step, lowering the overall performance of the workflow.
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
117
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
118 </help>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
119 <citations>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
120 <citation type="doi">10.1371/journal.pone.0168397</citation>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
121 </citations>
65d6d2b554b3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
artbio
parents:
diff changeset
122 </tool>