Mercurial > repos > iuc > purge_dups

annotate purge_dups.xml @ 2:17b378303f2d 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 3199d3f9c401663ffe45a679c3918489d4f6d149"
author iuc
date Tue, 27 Apr 2021 20:48:51 +0000
parents 29151e779524
children 76d4cbefff85
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
1 <tool id="purge_dups" name="Purge overlaps" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
2 <description>and haplotigs in an assembly based on read depth (purge_dups)</description>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
3 <macros>
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>
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
5 <token name="@VERSION_SUFFIX@">2</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":
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
12 #for $i, $file in enumerate($function_select.input):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
13 #if $file.is_of_type("paf"):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
14 gzip -c '${file}' > '${i}.gz' &&
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
15 #else
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
16 ln -s '${file}' '${i}.gz' &&
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
17 #end if
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
18 #end for
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
19 purge_dups
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
20 #if $function_select.coverage:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
21 -c '$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
22 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
23 #if $function_select.cutoffs:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
24 -T '$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
25 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
26 #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
27 -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
28 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
29 #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
30 -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
31 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
32 #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
33 -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
34 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
35 #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
36 -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
37 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
38 #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
39 -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
40 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
41 #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
42 -2
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.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
44 -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
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 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
47 #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
48 -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
49 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
50 #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
51 -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
52 #end if
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
53 #for $i, $file in enumerate($function_select.input):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
54 '${i}.gz'
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
55 #end for
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
56 > dups.bed 2> purge_dups.log
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
57 #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
58 split_fa
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
59 #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
60 -n $function_select.split
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
61 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
62 '$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
63 #else if $function_select.functions == "pbcstat":
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
64 #for $i, $file in enumerate($function_select.input):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
65 #if $file.is_of_type("paf"):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
66 gzip -c '${file}' > '${i}.gz' &&
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
67 #else
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
68 ln -s '${file}' '${i}.gz' &&
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
69 #end if
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
70 #end for
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
71 pbcstat
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
72 #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
73 -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
74 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
75 #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
76 -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
77 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
78 #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
79 -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
80 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
81 #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
82 -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
83 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
84 $function_select.primary_alignments
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
85 #for $i, $file in enumerate($function_select.input):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
86 '${i}.gz'
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
87 #end for
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
88 #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
89 ngscstat
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
90 #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
91 -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
92 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
93 ## #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
94 ## -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
95 ## #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
96 #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
97 -L $function_select.max_insert
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
98 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
99 '$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
100 #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
101 calcuts
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
102 #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
103 -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
104 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
105 #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
106 -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
107 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
108 #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
109 -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
110 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
111 #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
112 -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
113 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
114 $function_select.ploidy
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
115 '$function_select.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
116 #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
117 get_seqs
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
118 $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
119 $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
120 $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
121 $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
122 #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
123 -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
124 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
125 #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
126 -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
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 #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
129 -g $function_select.min_gap
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
130 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
131 '$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
132 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
133 ]]></command>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
134 <inputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
135 <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
136 <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
137 <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
138 <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
139 <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
140 <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
141 <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
142 <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
143 </param>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
144 <when value="purge_dups">
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
145 <param name="input" type="data" format="paf,paf.gz" multiple="true" 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
146 <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
147 <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
148 <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
149 <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
150 <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
151 <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
152 <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
153 <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
154 <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
155 <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
156 <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
157 </param>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
158 <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
159 <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
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="one"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
162 </conditional>
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="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
164 <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
165 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
166 <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
167 <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
168 <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
169 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
170 <when value="pbcstat">
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
171 <param name="input" type="data" format="paf,paf.gz" multiple="true" 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
172 <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"
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173 <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"
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diff changeset
174 <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
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diff changeset
175 <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"
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parents:
diff changeset
176 <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"
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parents:
diff changeset
177 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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parents:
diff changeset
178 <when value="ngscstat">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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diff changeset
179 <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"
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180 <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"
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diff changeset
181 <!-- 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"
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182 <!-- <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"
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diff changeset
183 <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"
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parents:
diff changeset
184 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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diff changeset
185 <when value="calcuts">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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186 <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"
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187 <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"
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188 <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"
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189 <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"
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190 <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"
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191 <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"
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192 <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"
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193 <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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194 </param>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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195 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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196 <when value="get_seqs">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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197 <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"
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198 <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"
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199 <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"
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200 <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"
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201 <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"
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202 <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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203 <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"
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diff changeset
204 <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"
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205 <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"
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diff changeset
206 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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207 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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208 </inputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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209 <outputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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210 <!-- Get Seqs -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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211 <data name="get_seqs_hap" format="fasta" from_work_dir="hap.fa" label="${tool.name} on ${on_string}: get seqs haplotype fasta" >
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
212 <filter>function_select['functions'] == 'get_seqs'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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diff changeset
213 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
214 <data name="get_seqs_purged" format="fasta" from_work_dir="purged.fa" label="${tool.name} on ${on_string}: get seqs purged fasta">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
215 <filter>function_select['functions'] == 'get_seqs'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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diff changeset
216 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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diff changeset
217 <!-- Split FA -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
218 <data name="split_fasta" format="fasta" from_work_dir="split.fasta" label="${tool.name} on ${on_string}: split fasta">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
219 <filter>function_select['functions'] == 'split_fa'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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diff changeset
220 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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diff changeset
221 <!-- Ngscstat -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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222 <data name="ngscstat_cov" format="tabular" from_work_dir="TX.base.cov" label="${tool.name} on ${on_string}: ngscstat base coverage file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
223 <filter>function_select['functions'] == 'ngscstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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224 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
225 <data name="ngscstat_stat" format="tabular" from_work_dir="TX.stat" label="${tool.name} on ${on_string}: ngscstat stat file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
226 <filter>function_select['functions'] == 'ngscstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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227 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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228 <!-- Pbcstat -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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229 <data name="pbcstat_cov" format="tabular" from_work_dir="PB.base.cov" label="${tool.name} on ${on_string}: pbcstat base coverage file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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diff changeset
230 <filter>function_select['functions'] == 'pbcstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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231 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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232 <data name="pbcstat_wig" format="wig" from_work_dir="PB.cov.wig" label="${tool.name} on ${on_string}: pbcstat base wig file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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233 <filter>function_select['functions'] == 'pbcstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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234 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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235 <data name="pbcstat_stat" format="tabular" from_work_dir="PB.stat" label="${tool.name} on ${on_string}: stat file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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236 <filter>function_select['functions'] == 'pbcstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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237 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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238 <!-- Calcuts -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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diff changeset
239 <data name="calcuts_log" format="txt" from_work_dir="calcuts.log" label="${tool.name} on ${on_string}: calcuts log file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
240 <filter>function_select['functions'] == 'calcuts'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
241 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
242 <data name="calcuts_tab" format="tabular" from_work_dir="cutoffs.tsv" label="${tool.name} on ${on_string}: calcuts cutoff file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
243 <filter>function_select['functions'] == 'calcuts'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
244 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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245 <!-- Purge dups -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
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246 <data name="purge_dups_log" format="txt" from_work_dir="purge_dups.log" label="${tool.name} on ${on_string}: purge_dups log file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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diff changeset
247 <filter>function_select['functions'] == 'purge_dups'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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248 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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249 <data name="purge_dups_bed" format="bed" from_work_dir="dups.bed" label="${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
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250 <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
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diff changeset
251 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
252 </outputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
253 <tests>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
254 <!-- Purge dups -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
255 <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
256 <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
257 <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
258 <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
259 <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
260 <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
261 <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
262 <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
263 <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
264 <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
265 <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
266 <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
267 <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
268 <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
269 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
270 <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
271 <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
272 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
273 <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
274 </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
275 <!-- 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
276 <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
277 <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
278 <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
279 <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
280 <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
281 <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
282 <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
283 <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
284 <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
285 <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
286 <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
287 <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
288 <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
289 <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
290 </conditional>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
291 <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
292 <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
293 </conditional>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
294 <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
295 </test>
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
296 <!-- Purge dups multiple input -->
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
297 <test expect_num_outputs="2">
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
298 <conditional name="function_select">
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
299 <param name="functions" value="purge_dups"/>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
300 <param name="input" value="test.paf,test2.paf.gz"/>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
301 </conditional>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
302 <output name="purge_dups_bed" value="purge_dups_out_2.bed"/>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
303 </test>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
304 <!-- Split fa -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
305 <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
306 <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
307 <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
308 <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
309 <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
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="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
312 </test>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
313 <!-- pbcstat -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
314 <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
315 <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
316 <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
317 <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
318 <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
319 <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
320 <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
321 <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
322 <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
323 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
324 <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
325 <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
326 </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
327 <!-- 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
328 <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
329 <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
330 <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
331 <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
332 <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
333 <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
334 <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
335 <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
336 <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
337 </conditional>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
338 <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
339 <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
340 </test>
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
341 <!-- Pbcstat multiple input -->
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
342 <test expect_num_outputs="3">
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
343 <conditional name="function_select">
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
344 <param name="functions" value="pbcstat"/>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
345 <param name="input" value="test.paf,test2.paf.gz"/>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
346 </conditional>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
347 <output name="pbcstat_cov" value="out2.cov"/>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
348 <output name="pbcstat_wig" value="out2.wig"/>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
349 </test>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
350 <!-- ngscstat -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
351 <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
352 <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
353 <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
354 <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
355 <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
356 <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
357 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
358 <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
359 </test>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
360 <!-- Calcuts -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
361 <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
362 <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
363 <param name="functions" value="calcuts"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
364 <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
parents:
diff changeset
365 <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
parents:
diff changeset
366 <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
parents:
diff changeset
367 <param name="transition" value="1"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
368 <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
parents:
diff changeset
369 <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
parents:
diff changeset
370 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
371 <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
parents:
diff changeset
372 </test>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
373 <!-- Get seqs -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
374 <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
375 <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
376 <param name="functions" value="get_seqs"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
377 <param name="fasta_input" value="split_out.fasta"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
378 <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
parents:
diff changeset
379 <param name="coverage" value="-c"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
380 <param name="length" value="10"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
381 <param name="haplotigs" value="-a"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
382 <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
parents:
diff changeset
383 <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
parents:
diff changeset
384 <param name="split" value="-s"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
385 <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
parents:
diff changeset
386 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
387 <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
parents:
diff changeset
388 </test>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
389 </tests>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
390 <help><![CDATA[
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
391 .. class:: infomark
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
392
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
393 **What it does**
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
394
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
395 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
parents:
diff changeset
396
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
397 ]]></help>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
398 <citations>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
399 <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:
diff changeset
400 </citations>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
401 </tool>