Mercurial > repos > iuc > purge_dups

annotate purge_dups.xml @ 1:29151e779524 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 6b395e598c4a02bb193895da5a2d9dd4240b1848"
author iuc
date Tue, 09 Mar 2021 18:25:07 +0000
parents 8ec117da1796
children 17b378303f2d
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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>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
4 <token name="@TOOL_VERSION@">1.2.5</token>
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
5 <token name="@VERSION_SUFFIX@">1</token>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
6 </macros>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
7 <requirements>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
9 </requirements>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
11 #if $function_select.functions == "purge_dups":
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
12 #if $function_select.input.is_of_type("paf"):
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
13 gzip -c '$function_select.input' > ./input.paf.gz &&
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
14 #end if
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
15 purge_dups
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
16 #if $function_select.coverage:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
17 -c '$function_select.coverage'
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
18 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
19 #if $function_select.cutoffs:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
20 -T '$function_select.cutoffs'
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
21 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
22 #if $function_select.min_bad:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
23 -f $function_select.min_bad
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
24 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
25 #if $function_select.min_align:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
26 -a $function_select.min_align
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
27 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
28 #if $function_select.min_match:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
29 -b $function_select.min_match
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
30 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
31 #if $function_select.min_chain:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
32 -m $function_select.min_chain
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
33 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
34 #if $function_select.max_gap:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
35 -M $function_select.max_gap
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
36 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
37 #if $function_select.double_chain.chaining_rounds == "two":
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
38 -2
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
39 #if $function_select.double_chain.max_gap_2:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
40 -G $function_select.double_chain.max_gap_2
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
41 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
42 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
43 #if $function_select.min_chain_score:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
44 -l $function_select.min_chain_score
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
45 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
46 #if $function_select.max_extend:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
47 -E $function_select.max_extend
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
48 #end if
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
49 #if $function_select.input.is_of_type("paf"):
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
50 'input.paf.gz' > dups.bed 2> purge_dups.log
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
51 #else:
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
52 '${function_select.input}' > dups.bed 2> purge_dups.log
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
53 #end if
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
54 #else if $function_select.functions == "split_fa":
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
55 split_fa
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
56 #if $function_select.split:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
57 -n $function_select.split
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
58 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
59 '$function_select.input' > split.fasta
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
60 #else if $function_select.functions == "pbcstat":
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
61 #if $function_select.input.is_of_type("paf"):
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
62 gzip -c '$function_select.input' > ./input.paf.gz &&
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
63 #end if
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
64 pbcstat
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
65 #if $function_select.max_cov:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
66 -M $function_select.max_cov
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
67 #end if
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.min_map_ratio:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
69 -f $function_select.min_map_ratio
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
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
71 #if $function_select.min_map_qual:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
72 -q $function_select.min_map_qual
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
73 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
74 #if $function_select.flank:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
75 -l $function_select.flank
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
76 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
77 $function_select.primary_alignments
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
78 #if $function_select.input.is_of_type("paf"):
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
79 'input.paf.gz'
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
80 #else:
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
81 '${function_select.input}'
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
82 #end if
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
83 #else if $function_select.functions == "ngscstat":
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
84 ngscstat
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
85 #if $function_select.min_align_qual:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
86 -q $function_select.min_align_qual
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
87 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
88 ## #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
89 ## -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
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 #if $function_select.max_insert:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
92 -L $function_select.max_insert
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
93 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
94 '$function_select.input'
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
95 #else if $function_select.functions == "calcuts":
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
96 calcuts
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
97 #if $function_select.min_depth:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
98 -f $function_select.min_depth
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
99 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
100 #if $function_select.low_depth:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
101 -l $function_select.low_depth
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
102 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
103 #if $function_select.transition:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
104 -m $function_select.transition
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
105 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
106 #if $function_select.upper_depth:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
107 -u $function_select.upper_depth
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
108 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
109 $function_select.ploidy
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
110 '$function_select.input' > cutoffs.tsv 2>calcuts.log
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
111 #else if $function_select.functions == "get_seqs":
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
112 get_seqs
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
113 $function_select.coverage
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
114 $function_select.haplotigs
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
115 $function_select.end_trim
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
116 $function_select.split
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
117 #if $function_select.length:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
118 -l $function_select.length
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
119 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
120 #if $function_select.min_ratio:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
121 -m $function_select.min_ratio
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
122 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
123 #if $function_select.min_gap:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
124 -g $function_select.min_gap
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
125 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
126 '$function_select.bed_input' '$function_select.fasta_input'
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
127 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
128 ]]></command>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
129 <inputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
130 <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
131 <param type="select" name="functions" label="Select the purge_dups function">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
132 <option value="purge_dups">purge haplotigs and overlaps for an assembly</option>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
133 <option value="split_fa">split FASTA file by 'N's</option>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
134 <option value="pbcstat">create read depth histogram and base-level read depth for pacbio data</option>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
135 <option value="ngscstat">create read depth histogram and base-level read detph for illumina data</option>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
136 <option value="calcuts">calculate coverage cutoffs</option>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
137 <option value="get_seqs">obtain seqeuences after purging</option>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
138 </param>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
139 <when value="purge_dups">
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
140 <param name="input" type="data" format="paf,paf.gz" label="PAF input file"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
141 <param name="coverage" type="data" format="tabular" optional="true" argument="-c" label="Base-level coverage file" />
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
142 <param name="cutoffs" type="data" format="tabular" label ="Cutoffs file" optional="true" argument="-T"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
143 <param name="min_bad" type="float" min="0" max="1" argument="-f" optional="true" label="Minimum fraction of haploid/diploid/bad/repetitive bases in a sequence" help="Default = 0.8"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
144 <param name="min_align" type="integer" label="Minimum alignment score" argument="-a" optional="true"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
145 <param name="min_match" type="integer" label="Minimum max match score" argument="-b" optional="true"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
146 <param name="min_chain" label="Minimum matching bases for chaining" type="integer" argument="-m" optional="true"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
147 <param name="max_gap" label="Maximum gap size for chaining" type="integer" argument="-M" optional="true"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
148 <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
149 <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
150 <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
151 <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
152 </param>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
153 <when value="two">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
154 <param name="max_gap_2" argument="-G" optional="true" label="Maximum gap size for second round of chaining" type="integer"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
155 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
156 <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
157 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
158 <param name="min_chain_score" argument="-l" optional="true" label="Minimum chaining score for a match" type="integer" />
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
159 <param name="max_extend" argument="-E" optional="true" label="Maximum extension for contig ends" type="integer" />
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
160 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
161 <when value="split_fa">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
162 <param name="input" type="data" format="fasta" label="Base-level coverage file"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
163 <param name="split" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Base-level coverage file" />
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
164 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
165 <when value="pbcstat">
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
166 <param name="input" type="data" format="paf,paf.gz" label="PAF input file"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
167 <param name="max_cov" type="integer" label="Maximum coverage" argument="-M" optional="true"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
168 <param name="min_map_ratio" argument="-f" type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
169 <param name="min_map_qual" type="integer" argument="-q" optional="true" label="Minimum mapping quality"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
170 <param name="flank" type="integer" argument="-l" optional="true" label="Flanking space" />
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
171 <param name="primary_alignments" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Use only primary alignments" />
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
172 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
173 <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
174 <param name="input" type="data" format="bam" label="BAM input file"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
175 <param name="min_align_qual" type="integer" argument="-q" optional="true" label="Minimum alignment quality" />
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
176 <!-- Param exists in help text, but isn't actually part of the code. Maybe in the next release? -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
177 <!-- <param name="max_depth" type="integer" label="Maximum read depth" argument="-M" optional="true"/> -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
178 <param name="max_insert" type="integer" argument="-L" optional="true" label="Maximum insert size"/>
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="calcuts">
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="tabular" label="STAT input file"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
182 <param name="min_depth" type="float" label="Minimum depth count fraction to maximum depth coun" min="0" max="1" argument="-f" optional="true" help="Default = 0.1"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
183 <param name="low_depth" label="Lower bound for read depth" type="integer" argument="-l" optional="true"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
184 <param name="transition" label="Transition between haploid and diploid" type="integer" argument="-m" optional="true"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
185 <param name="upper_depth" label="Upper bound for read depth" type="integer" argument="-u" optional="true"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
186 <param name="ploidy" argument="-d" type="select" label="Ploidy">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
187 <option value="-d 0" selected="true">Diploid [0]</option>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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188 <option value="-d 1">Haploid [1]</option>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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diff changeset
189 </param>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
190 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
191 <when value="get_seqs">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
192 <param name="fasta_input" type="data" format="fasta" label="Fasta input file"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
193 <param name="bed_input" type="data" format="bed" label="Bed input file"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
194 <param name="coverage" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Keep high coverage contigs in the primary contig set"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
195 <param name="haplotigs" type="boolean" argument="-a" truevalue="-a" falsevalue="" checked="false" label="Do not add prefix to haplotigs"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
196 <param name="length" type="integer" argument="-l" optional="true" label="Minimum primary contig length" help="Default: 1000"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
197 <param name="min_ratio" type="float" min="0" max="1" argument="-m" optional="true" label="Minimum ratio of remaining primary contig length to the original contig length"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
198 <param name="end_trim" type="boolean" argument="-e" truevalue="-e" falsevalue="" checked="true" label="Trim end sequences" help="Only remove sequences at end of halplotigs If you also want to remove the duplications in the middle, set to false, however that may delete false positive duplications."/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
199 <param name="split" type="boolean" argument="-s" truevalue="-s" falsevalue="" checked="false" label="Split contigs"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
200 <param name="min_gap" type="integer" argument="-g" optional="true" help="default=10k" label="Minimum gap size between duplications" />
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
201 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
202 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
203 </inputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
204 <outputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
205 <!-- Get Seqs -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
206 <data name="get_seqs_hap" format="fasta" from_work_dir="hap.fa" label="${tool.name} on ${on_string}: get seqs haplotype fasta" >
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
207 <filter>function_select['functions'] == 'get_seqs'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
208 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
209 <data name="get_seqs_purged" format="fasta" from_work_dir="purged.fa" label="${tool.name} on ${on_string}: get seqs purged fasta">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
210 <filter>function_select['functions'] == 'get_seqs'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
211 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
212 <!-- Split FA -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
213 <data name="split_fasta" format="fasta" from_work_dir="split.fasta" label="${tool.name} on ${on_string}: split fasta">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
214 <filter>function_select['functions'] == 'split_fa'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
215 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
216 <!-- Ngscstat -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
217 <data name="ngscstat_cov" format="tabular" from_work_dir="TX.base.cov" label="${tool.name} on ${on_string}: ngscstat base coverage file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
218 <filter>function_select['functions'] == 'ngscstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
219 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
220 <data name="ngscstat_stat" format="tabular" from_work_dir="TX.stat" label="${tool.name} on ${on_string}: ngscstat stat file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
221 <filter>function_select['functions'] == 'ngscstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
222 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
223 <!-- Pbcstat -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
224 <data name="pbcstat_cov" format="tabular" from_work_dir="PB.base.cov" label="${tool.name} on ${on_string}: pbcstat base coverage file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
225 <filter>function_select['functions'] == 'pbcstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
226 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
227 <data name="pbcstat_wig" format="wig" from_work_dir="PB.cov.wig" label="${tool.name} on ${on_string}: pbcstat base wig file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
228 <filter>function_select['functions'] == 'pbcstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
229 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
230 <data name="pbcstat_stat" format="tabular" from_work_dir="PB.stat" label="${tool.name} on ${on_string}: stat file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
231 <filter>function_select['functions'] == 'pbcstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
232 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
233 <!-- Calcuts -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
234 <data name="calcuts_log" format="txt" from_work_dir="calcuts.log" label="${tool.name} on ${on_string}: calcuts log file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
235 <filter>function_select['functions'] == 'calcuts'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
236 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
237 <data name="calcuts_tab" format="tabular" from_work_dir="cutoffs.tsv" label="${tool.name} on ${on_string}: calcuts cutoff file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
238 <filter>function_select['functions'] == 'calcuts'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
239 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
240 <!-- Purge dups -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
241 <data name="purge_dups_log" format="txt" from_work_dir="purge_dups.log" label="${tool.name} on ${on_string}: purge_dups log file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
242 <filter>function_select['functions'] == 'purge_dups'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
243 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
244 <data name="purge_dups_bed" format="bed" from_work_dir="dups.bed" label="${tool.name} on ${on_string}: purge_dups bed file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
245 <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
246 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
247 </outputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
248 <tests>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
249 <!-- Purge dups -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
250 <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
251 <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
252 <param name="functions" value="purge_dups"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
253 <param name="input" value="test.paf"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
254 <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
255 <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
256 <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
257 <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
258 <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
259 <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
260 <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
261 <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
262 <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
263 <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
264 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
265 <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
266 <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
267 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
268 <output name="purge_dups_bed" value="purge_dups_out.bed"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
269 </test>
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
270 <!-- Purge dups gzip -->
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
271 <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
272 <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
273 <param name="functions" value="purge_dups"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
274 <param name="input" value="test.paf.gz" ftype="paf.gz"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
275 <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
276 <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
277 <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
278 <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
279 <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
280 <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
281 <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
282 <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
283 <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
284 <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
285 </conditional>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
286 <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
287 <param name="max_extend" 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
288 </conditional>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
289 <output name="purge_dups_bed" value="purge_dups_out.bed"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
290 </test>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
291 <!-- Split fa -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
292 <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
293 <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
294 <param name="functions" value="split_fa"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
295 <param name="input" value="test.fasta"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
296 <param name="split" value="-n"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
297 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
298 <output name="split_fasta" 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
299 </test>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
300 <!-- pbcstat -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
301 <test expect_num_outputs="3">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
302 <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
303 <param name="functions" value="pbcstat"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
304 <param name="input" value="test.paf"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
305 <param name="max_cov" value="1000"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
306 <param name="min_map_ratio" 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
307 <param name="min_map_qual" value="1"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
308 <param name="flank" value="1"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
309 <param name="primary_alignments" value="-p"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
310 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
311 <output name="pbcstat_cov" value="out.cov"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
312 <output name="pbcstat_wig" value="out.wig"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
313 </test>
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 <!-- pbcstat gzip -->
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
315 <test expect_num_outputs="3">
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
316 <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
317 <param name="functions" value="pbcstat"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
318 <param name="input" value="test.paf.gz" ftype="paf.gz"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
319 <param name="max_cov" 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
320 <param name="min_map_ratio" 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
321 <param name="min_map_qual" 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
322 <param name="flank" 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
323 <param name="primary_alignments" value="-p"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
324 </conditional>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
325 <output name="pbcstat_cov" value="out.cov"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
326 <output name="pbcstat_wig" value="out.wig"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
327 </test>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
328 <!-- ngscstat -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
329 <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
330 <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
331 <param name="functions" value="ngscstat"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
332 <param name="input" value="test.bam"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
333 <param name="min_align_qual" value="10"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
334 <param name="max_insert" value="100"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
335 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
336 <output name="ngscstat_cov" value="ngsc_out.cov"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
337 </test>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
338 <!-- Calcuts -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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339 <test expect_num_outputs="2">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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340 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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341 <param name="functions" value="calcuts"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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342 <param name="input" value="test.stat"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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343 <param name="min_depth" value="0.01"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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344 <param name="low_depth" value="1"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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345 <param name="transition" value="1"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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346 <param name="upper_depth" value="100"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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347 <param name="ploidy" value="-d 0"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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348 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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349 <output name="calcuts_tab" value="calcuts_out.tsv"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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350 </test>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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351 <!-- Get seqs -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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352 <test expect_num_outputs="2">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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353 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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354 <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
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355 <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
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356 <param name="bed_input" value="dups.bed"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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357 <param name="coverage" value="-c"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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358 <param name="length" value="10"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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359 <param name="haplotigs" value="-a"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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360 <param name="min_ratio" value=".01"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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361 <param name="end_trim" value="-e"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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362 <param name="split" value="-s"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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363 <param name="min_gap" value="100000"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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364 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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365 <output name="get_seqs_purged" value="purged_out.fa"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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366 </test>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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367 </tests>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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368 <help><![CDATA[
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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369 .. class:: infomark
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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370
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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371 **What it does**
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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372
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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373 The purge_dups tools are designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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374
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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375 ]]></help>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
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376 <citations>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
377 <citation type="doi">10.1093/bioinformatics/btaa025</citation>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
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378 </citations>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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379 </tool>