Mercurial > repos > iuc > purge_dups

annotate purge_dups.xml @ 4:a315c25dc813 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/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
author iuc
date Tue, 12 Oct 2021 19:07:05 +0000
parents 76d4cbefff85
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
1 <tool id="purge_dups" name="Purge overlaps" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
2 <description>and haplotigs in an assembly based on read depth (purge_dups)</description>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
3 <macros>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
4 <import>macros.xml</import>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
5 </macros>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
6 <expand macro="xrefs"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
7 <expand macro="requirements"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
9 #if $function_select.functions == 'purge_dups':
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
10 #for $i, $file in enumerate($function_select.input):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
11 #if $file.is_of_type("paf"):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
12 gzip -c '${file}' > '${i}.gz' &&
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
13 #else
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
14 ln -s '${file}' '${i}.gz' &&
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
15 #end if
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
16 #end for
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
17 purge_dups
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
18 #if $function_select.coverage:
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
19 -c '${function_select.coverage}'
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
20 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
21 #if $function_select.cutoffs:
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
22 -T '${function_select.cutoffs}'
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
23 #end if
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
24 -f $function_select.min_bad
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
25 -a $function_select.min_align
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
26 -b $function_select.min_match
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
27 -m $function_select.min_chain
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
28 -M $function_select.max_gap
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
29 #if $function_select.double_chain.chaining_rounds == 'two':
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
30 -2
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
31 -G $function_select.double_chain.max_gap_2
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
32 #end if
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
33 -l $function_select.min_chain_score
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
34 -E $function_select.max_extend
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
35 #for $i, $file in enumerate($function_select.input):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
36 '${i}.gz'
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
37 #end for
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
38 > dups.bed 2> purge_dups.log
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
39 #else if $function_select.functions == 'split_fa':
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
40 split_fa
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
41 '${function_select.input}' > split.fasta
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
42 #else if $function_select.functions == 'pbcstat':
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
43 #for $i, $file in enumerate($function_select.input):
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
44 #if $file.is_of_type('paf'):
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
45 gzip -c '${file}' > '${i}.gz' &&
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
46 #else
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
47 ln -s '${file}' '${i}.gz' &&
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
48 #end if
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
49 #end for
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
50 pbcstat
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
51 -M $function_select.pbcstat_options.max_cov
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
52 -f $function_select.pbcstat_options.min_map_ratio
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
53 #if $function_select.pbcstat_options.min_map_qual:
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
54 -q $function_select.pbcstat_options.min_map_qual
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
55 #end if
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
56 -l $function_select.pbcstat_options.flank
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
57 $function_select.pbcstat_options.primary_alignments
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
58 #for $i, $file in enumerate($function_select.input):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
59 '${i}.gz'
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
60 #end for
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
61 && mv PB.stat depth.stat
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
62 && @CALCUTS@ depth.stat > cutoffs.tsv 2>calcuts.log
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
63 && @HIST_PLOT@
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
64
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
65 #else if $function_select.functions == 'ngscstat':
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
66 ngscstat
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
67 -q $function_select.ngscstat_options.min_align_qual
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
68 ## #if $function_select.max_depth:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
69 ## -M $function_select.max_depth
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
70 ## #end if
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
71 -L $function_select.ngscstat_options.max_insert
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
72 '${function_select.input}'
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
73 && mv TX.stat depth.stat
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
74 && @CALCUTS@ depth.stat > cutoffs.tsv 2>calcuts.log
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
75 && @HIST_PLOT@
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
76
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
77 #else if $function_select.functions == 'calcuts':
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
78 @CALCUTS@ '${function_select.input}' > cutoffs.tsv 2>calcuts.log
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
79
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
80 #else if $function_select.functions == 'get_seqs':
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
81 get_seqs
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
82 $function_select.advanced_options.coverage
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
83 $function_select.advanced_options.haplotigs
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
84 $function_select.advanced_options.end_trim
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
85 $function_select.advanced_options.split
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
86 -l $function_select.advanced_options.length
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
87 -m $function_select.advanced_options.min_ratio
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
88 -g $function_select.advanced_options.min_gap
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
89 '${function_select.bed_input}' '${function_select.fasta_input}'
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
90 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
91 ]]></command>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
92 <inputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
93 <conditional name="function_select">
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
94 <param type="select" name="functions" label="Function mode">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
95 <option value="pbcstat">Calculate coverage cutoff, base-level read depth and create read depth histogram for PacBio data (calcuts+pbcstat)</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
96 <option value="ngscstat">Calculate coverage cutoff, base-level read depth and create read depth histogram for Illumina data (calcuts+ngscstat)</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
97 <option value="calcuts">Calculate coverage cutoffs (calcuts)</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
98 <option value="split_fa">Split assembly FASTA files by 'N's (split_fa)</option>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
99 <option value="purge_dups">Purge haplotigs and overlaps for an assembly (purge_dups)</option>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
100 <option value="get_seqs">Obtain sequences after purging (get_seqs)</option>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
101 </param>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
102 <when value="purge_dups">
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
103 <param name="input" type="data" format="paf,paf.gz" multiple="true" label="PAF input file"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
104 <param argument="-c" name="coverage" type="data"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
105 format="tabular" optional="true" label="Base-level coverage file"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
106 help="This file is generated with purge_dups by using the 'Calculate coverage cutoff, base-level
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
107 read depth and create read depth histogram' option"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
108 <param argument="-T" name="cutoffs" type="data"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
109 format="tabular" optional="true" label ="Cutoffs file"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
110 help="This file is generated with purge_dups by using the 'Calculate coverage cutoff, base-level
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
111 read depth and create read depth histogram' option"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
112 <param argument="-f" name="min_bad" type="float"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
113 min="0" max="1" value="0.8" label="Minimum fraction of haploid/diploid/bad/repetitive bases in a sequence"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
114 help="This parameter is set for a suspect haplotigs. If 80% (default value) of a scaffold is high coverage
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
115 (defined by the sixth column of the cutoff file), it's a repetitive contig. If 80% is low coverage (defined
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
116 in the first column of the cutoff file), it's a junk contig. If 80% is above diploid coverage(defined in
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
117 the fourth column of the cutoff file), it's a diploid, otherwise it's a suspect haplotig"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
118 <param argument="-a" name="min_align" type="integer"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
119 min="0" value="70" label="Minimum alignment score"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
120 help="If its alignment score is larger than this parameter and max match score larger than
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
121 the 'mininum max match score' (-b), it is marked as a repeat; if the alignment score is larger than this parameter
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
122 and max match score no larger than the 'mininum max match score', it is marked as a haplotig.
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
123 Otherwise it is left as a candidate primary contig. If after purging, the complete genes reported by BUSCO are
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
124 too low, you can try to increase this parameter"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
125 <param argument="-b" name="min_match" type="integer"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
126 min="0" value="200" label="Minimum max match score"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
127 help="If its alignment score is larger than the 'minimum align score' (-a) and max match score larger than
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
128 this parameter, it is marked as a repeat; if the alignment score is larger than the 'minimum
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
129 align' and max match score no larger than this parameter, it is marked as a haplotig.
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
130 Otherwise it is left as a candidate primary contig."/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
131 <param argument="-m" name="min_chain" type="integer"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
132 min="0" value="500" label="Minimum matching bases for chaining"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
133 help="In the first round, it will asset chains consistent alignments within this parameter value"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
134 <param argument="-M" name="max_gap" type="integer"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
135 min="0" value="20000" label="Maximum gap size for chaining"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
136 help="In the first round, it will asset chains consistent alignments within this parameter value"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
137 <conditional name="double_chain">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
138 <param type="select" name="chaining_rounds" label="Rounds of chaining">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
139 <option value="one">1 round</option>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
140 <option value="two">2 rounds</option>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
141 </param>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
142 <when value="two">
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
143 <param argument="-G" name="max_gap_2" type="integer"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
144 min="0" value="50000" label="Maximum gap size for second round of chaining"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
145 help="In the second round, it will asset chains consistent alignments within this parameter value"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
146 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
147 <when value="one"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
148 </conditional>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
149 <param argument="-l" name="min_chain_score" type="integer"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
150 min="0" value="10000" label="Minimum chaining score for a match"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
151 help="This parameter control the overlap size. You should decrease its value to allow more overlaps"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
152 <param argument="-E" name="max_extend" type="integer"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
153 min="0" value="15000" label="Maximum extension for contig ends"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
154 help="If the chained alignment is within this value to the contig ends, it will extended to the ends"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
155 <param name="log_file" type="boolean" truevalue="true" falsevalue="false" label="Generate log file"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
156 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
157 <when value="split_fa">
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
158 <param name="input" type="data" format="fasta,fasta.gz" label="Assembly FASTA file" help="The sequence will be cleaved in those position in which the nucleotides is an 'N' or an 'n'."/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
159 <!-- This option disables the cleaving process, and yield the original sequence
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
160 <param argument="-n" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Block split by N" help="Enable this option if you do not want break your scaffols into contigs."/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
161 -->
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
162 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
163 <when value="pbcstat">
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
164 <param name="input" type="data" format="paf,paf.gz" multiple="true" label="PAF input file"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
165 <section name="pbcstat_options" title="PBCSTAT options" expanded="true">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
166 <param argument="-M" name="max_cov" type="integer" min="0" value="500" label="Maximum coverage"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
167 <param argument="-f" name="min_map_ratio" type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
168 <param argument="-q" name="min_map_qual" type="integer" optional="true" label="Minimum mapping quality"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
169 <param argument="-l" name="flank" type="integer" min="0" value="0" label="Flanking space" />
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
170 <param argument="-p" name="primary_alignments" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Use only primary alignments" />
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
171 </section>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
172 <expand macro="calcuts" />
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
173 <expand macro="trimmers"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
174 <expand macro="output_macro">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
175 <option value="pbcstat_coverage" selected="true">PBCSTAT base coverage</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
176 <option value="pbcstat_wig">PBCSTAT base coverage (WIG)</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
177 <option value="depth_stats">PBCSTAT depths</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
178 </expand>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
179 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
180 <when value="ngscstat">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
181 <param name="input" type="data" format="bam" label="BAM input file"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
182 <section name="ngscstat_options" title="NGSCSTAT options" expanded="true">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
183 <param argument="-q" name="min_align_qual" type="integer" min="0" value="30" label="Minimum alignment quality" />
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
184 <!-- Param exists in help text, but isn't actually part of the code. Maybe in the next release? -->
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
185 <!-- <param name="max_depth" type="integer" label="Maximum read depth" argument="-M" optional="true"/> -->
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
186 <param argument="-L" name="max_insert" type="integer" min="0" value="1000" label="Maximum insert size"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
187 </section>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
188 <expand macro="calcuts" />
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
189 <expand macro="trimmers"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
190 <expand macro="output_macro">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
191 <option value="ngscstat_coverage" selected="true">NGSCSTAT base coverage</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
192 </expand>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
193 </when>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
194
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
195 <when value="calcuts">
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
196 <param name="input" type="data" format="tabular" label="Depths input file"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
197 <expand macro="calcuts" />
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
198 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
199 <when value="get_seqs">
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
200 <param name="fasta_input" type="data" format="fasta" label="Assembly FASTA file"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
201 <param name="bed_input" type="data" format="bed" label="BED input file" help="Generated by the 'purge_dups' function mode."/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
202 <section name="advanced_options" title="Advanced options">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
203 <param argument="-c" name="coverage" type="boolean"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
204 truevalue="-c" falsevalue="" checked="false" label="Keep high coverage contigs in the primary contig set"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
205 <param argument="-a" name="haplotigs" type="boolean" truevalue="-a" falsevalue="" checked="false" label="Do not add prefix to haplotigs"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
206 <param argument="-l" name="length" type="integer" min="0" value="10000" label="Minimum primary contig length" />
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
207 <param argument="-m" name="min_ratio" type="float"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
208 min="0" max="1" value="0.05" label="Minimum ratio of remaining primary contig length to the original contig length"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
209 <param argument="-e" name="end_trim" type="boolean"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
210 truevalue="-e" falsevalue="" checked="true" label="Trim end sequences"
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
211 help="Only remove sequences at end of halplotigs. If you also want to remove the duplications in the middle,
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
212 set to false, however that may delete false positive duplications."/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
213 <param argument="-s" name="split" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Split contigs"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
214 <param argument="-g" name="min_gap" type="integer" min="0" value="10000" label="Minimum gap size between duplications" />
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
215 </section>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
216 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
217 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
218 </inputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
219 <outputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
220 <!-- Get Seqs -->
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
221 <data name="get_seqs_hap" format="fasta" from_work_dir="hap.fa" label="${tool.name} on ${on_string}: get_seqs haplotype" >
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
222 <filter>function_select['functions'] == 'get_seqs'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
223 </data>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
224 <data name="get_seqs_purged" format="fasta" from_work_dir="purged.fa" label="${tool.name} on ${on_string}: get_seqs purged sequences">
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
225 <filter>function_select['functions'] == 'get_seqs'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
226 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
227 <!-- Split FA -->
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
228 <data name="split_fasta" format="fasta" from_work_dir="split.fasta" label="${tool.name} on ${on_string}: split FASTA">
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
229 <filter>function_select['functions'] == 'split_fa'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
230 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
231 <!-- Ngscstat -->
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
232 <data name="ngscstat_cov" format="tabular" from_work_dir="TX.base.cov" label="${tool.name} on ${on_string}: NGSCSTAT base coverage">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
233 <filter>function_select['functions'] == 'ngscstat'</filter>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
234 <filter>'ngscstat_coverage' in function_select['output_options']</filter>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
235 </data>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
236 <data name="stat_file" format="tabular" from_work_dir="depth.stat" label="${tool.name} on ${on_string}: depths">
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
237 <filter>function_select['functions'] == 'ngscstat' or function_select['functions'] == 'pbcstat'</filter>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
238 <filter>'depth_stats' in function_select['output_options']</filter>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
239 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
240 <!-- Pbcstat -->
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
241 <data name="pbcstat_cov" format="tabular" from_work_dir="PB.base.cov" label="${tool.name} on ${on_string}: PBCSTAT base coverage">
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
242 <filter>function_select['functions'] == 'pbcstat'</filter>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
243 <filter>'pbcstat_coverage' in function_select['output_options']</filter>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
244 </data>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
245 <data name="pbcstat_wig" format="wig" from_work_dir="PB.cov.wig" label="${tool.name} on ${on_string}: PBCSTAT base coverage (WIG)">
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
246 <filter>function_select['functions'] == 'pbcstat'</filter>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
247 <filter>'pbcstat_wig' in function_select['output_options']</filter>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
248 </data>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
249
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
250 <data name="hist" format="png" from_work_dir="hist.png" label="${tool.name} on ${on_string}: histogram plot">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
251 <filter>function_select['functions'] == 'pbcstat' or function_select['functions'] == 'ngscstat'</filter>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
252 <filter>'histogram' in function_select['output_options']</filter>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
253 </data>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
254
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
255 <!-- Calcuts -->
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
256 <data name="calcuts_log" format="txt" from_work_dir="calcuts.log" label="${tool.name} on ${on_string}: calcuts log">
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
257 <filter>function_select['functions'] in ('pbcstat', 'ngscstat', 'calcuts')</filter>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
258 <filter>'calcuts_log' in function_select['output_options']</filter>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
259 </data>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
260 <data name="calcuts_cutoff" format="tabular" from_work_dir="cutoffs.tsv" label="${tool.name} on ${on_string}: calcuts cutoff">
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
261 <filter>function_select['functions'] in ('pbcstat', 'ngscstat', 'calcuts')</filter>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
262 <filter>'calcuts_cutoff' in function_select['output_options']</filter>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
263 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
264 <!-- Purge dups -->
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
265 <data name="purge_dups_log" format="txt" from_work_dir="purge_dups.log" label="${tool.name} on ${on_string}: purge_dups log">
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
266 <filter>function_select['functions'] == 'purge_dups'</filter>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
267 <filter>function_select['log_file']</filter>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
268 </data>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
269 <data name="purge_dups_bed" format="bed" from_work_dir="dups.bed" label="${tool.name} on ${on_string}: purge_dups BED">
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
270 <filter>function_select['functions'] == 'purge_dups'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
271 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
272 </outputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
273 <tests>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
274 <!-- Test 1 Purge dups -->
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
275 <test expect_num_outputs="1">
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
276 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
277 <param name="functions" value="purge_dups"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
278 <param name="input" value="assembly_test.paf"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
279 <param name="coverage" value="test.cov" ftype="tabular"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
280 <param name="cutoffs" value="cutoffs.tsv" ftype="tabular"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
281 <param name="min_bad" value="0.01"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
282 <param name="min_align" value="10"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
283 <param name="min_match" value="100"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
284 <param name="min_chain" value="1"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
285 <param name="max_gap" value="1000"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
286 <conditional name="double_chain">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
287 <param name="chaining_rounds" value="two"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
288 <param name="max_gap_2" value="1001"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
289 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
290 <param name="min_chain_score" value="1"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
291 <param name="max_extend" value="100"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
292 </conditional>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
293 <output name="purge_dups_bed" value="purge_dups_01.bed" ftype="bed"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
294 </test>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
295 <!-- Test 2 Purge dups gzip -->
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
296 <test expect_num_outputs="2">
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
297 <conditional name="function_select">
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
298 <param name="functions" value="purge_dups"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
299 <param name="input" value="assembly_test.paf.gz" ftype="paf.gz"/>
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
300 <param name="coverage" value="test.cov" ftype="tabular"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
301 <param name="cutoffs" value="cutoffs.tsv" ftype="tabular"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
302 <param name="min_bad" value="0.01"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
303 <param name="min_align" value="10"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
304 <param name="min_match" value="100"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
305 <param name="min_chain" value="1"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
306 <param name="max_gap" value="1000"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
307 <conditional name="double_chain">
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
308 <param name="chaining_rounds" value="two"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
309 <param name="max_gap_2" value="1001"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
310 </conditional>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
311 <param name="min_chain_score" value="1"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
312 <param name="max_extend" value="100"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
313 <param name="log_file" value="true"/>
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
314 </conditional>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
315 <output name="purge_dups_bed" value="purge_dups_02.bed" ftype="bed"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
316 <output name="purge_dups_log" value="purge_dups_log_02.txt" ftype="txt"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
317
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
318 </test>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
319 <!-- Test 3 Purge dups multiple input -->
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
320 <test expect_num_outputs="1">
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
321 <conditional name="function_select">
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
322 <param name="functions" value="purge_dups"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
323 <param name="input" value="assembly_test.paf,test2.paf.gz"/>
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
324 </conditional>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
325 <output name="purge_dups_bed" value="purge_dups_03.bed" ftype="bed"/>
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
326 </test>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
327 <!-- Test 4 Split fa -->
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
328 <test expect_num_outputs="1">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
329 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
330 <param name="functions" value="split_fa"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
331 <param name="input" value="assembly_test.fasta"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
332 </conditional>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
333 <output name="split_fasta" value="split_04.fasta" ftype="fasta"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
334 </test>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
335 <!-- Test 5 pbcstat -->
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
336 <test expect_num_outputs="6">
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
337 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
338 <param name="functions" value="pbcstat"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
339 <param name="input" value="assembly_test.paf"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
340 <section name="pbcstat_options">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
341 <param name="max_cov" value="1000"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
342 <param name="min_map_ratio" value="0.01"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
343 <param name="min_map_qual" value="1"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
344 <param name="flank" value="1"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
345 <param name="primary_alignments" value="-p"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
346 </section>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
347 <section name="section_calcuts">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
348 <param name="min_depth" value="0.01"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
349 <param name="low_depth" value="1"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
350 <param name="transition" value="1"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
351 <param name="upper_depth" value="100"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
352 <param name="ploidy" value="-d 0"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
353 </section>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
354 <param name="output_options" value="pbcstat_coverage,pbcstat_wig,depth_stats,histogram,calcuts_cutoff,calcuts_log"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
355 </conditional>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
356 <output name="calcuts_cutoff" value="calcuts_cutoff_05.tabular" ftype="tabular"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
357 <output name="calcuts_log" value="calcuts_log_05.txt" ftype="txt"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
358 <output name="pbcstat_cov" value="pbcstat_cov_05.tabular" ftype="tabular"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
359 <output name="pbcstat_wig" value="pbcstat_cov_05.wig" ftype="wig"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
360 <output name="stat_file" value="pbcstats_05.tabular" ftype="tabular"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
361 <output name="hist" value="hist_05.png" ftype="png" compare="sim_size"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
362 </test>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
363 <!-- Test 6 pbcstat gzip -->
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
364 <test expect_num_outputs="2">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
365 <conditional name="function_select">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
366 <param name="functions" value="pbcstat"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
367 <param name="input" value="assembly_test.paf.gz" ftype="paf.gz"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
368 <section name="pbcstat_options">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
369 <param name="max_cov" value="1000"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
370 <param name="min_map_ratio" value="0.01"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
371 <param name="min_map_qual" value="1"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
372 <param name="flank" value="1"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
373 <param name="primary_alignments" value="-p"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
374 </section>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
375 <section name="section_calcuts">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
376 <param name="min_depth" value="0.01"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
377 <param name="low_depth" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
378 <param name="transition" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
379 <param name="upper_depth" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
380 <param name="ploidy" value="-d 0"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
381 </section>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
382 </conditional>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
383 <param name="output_options" value="pbcstat_coverage,calcuts_cutoff"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
384 <output name="calcuts_cutoff" value="calcuts_cutoff_06.tabular" ftype="tabular"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
385 <output name="pbcstat_cov" value="pbcstat_cov_06.tabular" ftype="tabular"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
386 </test>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
387 <!-- Test 7 Pbcstat multiple input -->
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
388 <test expect_num_outputs="2">
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
389 <conditional name="function_select">
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
390 <param name="functions" value="pbcstat"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
391 <param name="input" value="assembly_test.paf,test2.paf.gz"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
392 <section name="section_calcuts">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
393 <param name="min_depth" value="0.01"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
394 <param name="low_depth" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
395 <param name="transition" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
396 <param name="upper_depth" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
397 <param name="ploidy" value="-d 0"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
398 </section>
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
399 </conditional>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
400 <param name="output_options" value="pbcstat_coverage,calcuts_cutoff"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
401 <output name="calcuts_cutoff" value="calcuts_cutoff_07.tabular" ftype="tabular"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
402 <output name="pbcstat_cov" value="pbcstat_cov_07.tabular" ftype="tabular"/>
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
403 </test>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
404 <!-- Test 8 ngscstat -->
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
405 <test expect_num_outputs="2">
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
406 <conditional name="function_select">
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
407 <param name="functions" value="ngscstat"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
408 <param name="input" value="test.bam"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
409 <section name="ngscstat_options">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
410 <param name="min_align_qual" value="10"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
411 <param name="max_insert" value="100"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
412 </section>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
413 <section name="section_calcuts">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
414 <param name="min_depth" value="0.01"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
415 <param name="low_depth" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
416 <param name="transition" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
417 <param name="upper_depth" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
418 <param name="ploidy" value="-d 0"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
419 </section>
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
420 </conditional>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
421 <param name="output_options" value="ngscstat_coverage,calcuts_cutoff"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
422 <output name="calcuts_cutoff" value="calcuts_cutoff_08.tabular" ftype="tabular"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
423 <output name="ngscstat_cov" value="ngsc_cov_08.tabular" ftype="tabular"/>
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
424 </test>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
425 <!-- Test 9 Calcuts -->
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
426 <test expect_num_outputs="2">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
427 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
428 <param name="functions" value="calcuts"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
429 <param name="input" value="test.stat"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
430 <section name="section_calcuts">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
431 <param name="min_depth" value="0.01"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
432 <param name="low_depth" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
433 <param name="transition" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
434 <param name="upper_depth" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
435 <param name="ploidy" value="-d 0"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
436 </section>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
437 </conditional>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
438 <output name="calcuts_cutoff" value="calcuts_cutoff_09.tabular" ftype="tabular"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
439 <output name="calcuts_log" value="calcuts_log_09.txt" ftype="txt"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
440 </test>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
441 <!-- Test 10 Get seqs -->
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
442 <test expect_num_outputs="2">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
443 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
444 <param name="functions" value="get_seqs"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
445 <param name="fasta_input" value="split_out.fasta"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
446 <param name="bed_input" value="dups.bed"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
447 <section name="advanced_options">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
448 <param name="coverage" value="-c"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
449 <param name="length" value="10"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
450 <param name="haplotigs" value="-a"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
451 <param name="min_ratio" value=".01"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
452 <param name="end_trim" value="-e"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
453 <param name="split" value="-s"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
454 <param name="min_gap" value="100000"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
455 </section>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
456 </conditional>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
457 <output name="get_seqs_purged" value="get_seqs_purged_10.fa" ftype="fasta"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
458 <output name="get_seqs_hap" value="get_seqs_hap_10.fa" ftype="fasta"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
459 </test>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
460 <!-- Test 11 pbcstat histogram options-->
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
461 <test expect_num_outputs="1">
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
462 <conditional name="function_select">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
463 <param name="functions" value="pbcstat"/>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
464 <param name="input" value="assembly_test.paf"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
465 <section name="pbcstat_options">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
466 <param name="max_cov" value="1000"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
467 <param name="min_map_ratio" value="0.01"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
468 <param name="min_map_qual" value="1"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
469 <param name="flank" value="1"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
470 <param name="primary_alignments" value="-p"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
471 </section>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
472 <section name="section_calcuts">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
473 <param name="min_depth" value="0.01"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
474 <param name="low_depth" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
475 <param name="transition" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
476 <param name="upper_depth" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
477 <param name="ploidy" value="-d 0"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
478 </section>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
479 <section name="section_hist">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
480 <param name="ymax" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
481 <param name="xmax" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
482 <param name="cutoffs_his" value="calcuts_out.tsv"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
483 </section>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
484 </conditional>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
485 <param name="output_options" value="histogram"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
486 <output name="hist" value="hist_11.png" ftype="png" compare="sim_size"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
487 </test>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
488 </tests>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
489 <help><![CDATA[
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
490 .. class:: infomark
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
491
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
492 **Purpose**
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
493
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
494 The purge_dups tools are designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
495 purge_dups can significantly improve genome assemblies by removing overlaps and haplotigs caused by sequence divergence
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
496 in heterozygous regions. This both removes false duplications in primary draft assemblies while retaining completeness and sequence
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
497 integrity, and can improve scaffolding.
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
498
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
499 ----
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
500
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
501 .. class:: infomark
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
502
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
503 **Pipeline Guide**
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
504
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
505 Given a primary assembly, and an alternative assembly (optional, if you have one), follow the steps shown below to build your
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
506 own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 5 is optional,
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
507 we highly recommend our users to do so, because assemblers may produce overrepresented sequences. In such a case, the final
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
508 step 5 can be applied to remove those seqeuences.
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
509
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
510 - Step 1: Calculate the coverage cutoffs and base coverages.
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
511 - Step 2: Split an assembly with the **split_fasfa** function and do a self-self alignment by using minimap2.
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
512 - Step 3: Purge haplotigs and overlaps with the **purge_dups** function.
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
513 - Step 4: Get purged primary and haplotig sequences from the draft assembly with the **get_seqs** function.
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
514 - Step 5: Merge hap.fa file, generated in the previous step, and the alternate assembly, and redo the above steps to get a decent haplotig set.
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
515
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
516 ----
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
517
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
518 .. class:: infomark
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
519
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
520 **Limitations**
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
521
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
522 - Read depth cutoffs calculation: the coverage cutoffs can be larger for a low heterozygosity species, which causes the purged assembly size smaller than expected. In such a case, please use script/hist_plot.py to make the histogram plot and set coverage cutoffs manually.
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
523 - Repeats: purge_dups has a limited ability to process repeats.
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
524
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
525 ----
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
526
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
527 .. class:: infomark
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
528
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
529 **Purged assembly validation**
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
530
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
531 There are many ways to validate the purged assembly. One way is to make a coverage plot for it, the 2nd way is to run `BUSCO <https://busco.ezlab.org/>`_. A thid option is to use `Merqury <https://github.com/marbl/merqury>`_
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
532
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
533
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
534
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
535 ]]></help>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents: 3
diff changeset
536 <expand macro="citations"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
537 </tool>