Mercurial > repos > bebatut > cdhit

annotate cdhit_macros.xml @ 4:ba7e9a012723 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 4a97d14fadd86dda8abd088023c7f9f2dcab2a88
author bebatut
date Fri, 04 May 2018 05:40:24 -0400
parents 626cd6334dbc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
1 <macros>
2
aa923171e225 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 8b1037213553ecffa32f15a499407cba816ab62b-dirty
bebatut
parents: 0
diff changeset
2 <xml name="requirements">
aa923171e225 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 8b1037213553ecffa32f15a499407cba816ab62b-dirty
bebatut
parents: 0
diff changeset
3 <requirements>
aa923171e225 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 8b1037213553ecffa32f15a499407cba816ab62b-dirty
bebatut
parents: 0
diff changeset
4 <requirement type="package" version="4.6.4">cd-hit</requirement>
aa923171e225 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 8b1037213553ecffa32f15a499407cba816ab62b-dirty
bebatut
parents: 0
diff changeset
5 </requirements>
aa923171e225 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 8b1037213553ecffa32f15a499407cba816ab62b-dirty
bebatut
parents: 0
diff changeset
6 </xml>
aa923171e225 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 8b1037213553ecffa32f15a499407cba816ab62b-dirty
bebatut
parents: 0
diff changeset
7
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
8 <template name="common_cdhit_options">
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
9 #if $advanced.settings == 'yes':
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
10
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
11 #if str($advanced.band_width) != 'None':
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
12 -b $advanced.band_width
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
13 #end if
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
14
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
15 #if str($advanced.throw_away_len) != 'None':
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
16 -l $advanced.throw_away_len
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
17 #end if
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
18
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
19 #if str($advanced.description_len) != 'None':
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
20 -d $advanced.description_len
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
21 #end if
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
22
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
23 #if str($advanced.cutoff_diff_len) != 'None':
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
24 -s $advanced.cutoff_diff_len
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
25 #end if
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
26
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
27 #if str($advanced.aa_cutoff_diff_len) != 'None':
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
28 -S $advanced.aa_cutoff_diff_len
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
29 #end if
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
30
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
31 #if $advanced.align.style == 'local':
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
32 -G 0
4
ba7e9a012723 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 4a97d14fadd86dda8abd088023c7f9f2dcab2a88
bebatut
parents: 3
diff changeset
33 #if str($advanced.align.align_coverage_long) != 'None':
ba7e9a012723 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 4a97d14fadd86dda8abd088023c7f9f2dcab2a88
bebatut
parents: 3
diff changeset
34 -aL $advanced.align.align_coverage_long
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
35 #end if
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
36
4
ba7e9a012723 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 4a97d14fadd86dda8abd088023c7f9f2dcab2a88
bebatut
parents: 3
diff changeset
37 #if str($advanced.align.align_coverage_long_control) != 'None':
ba7e9a012723 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 4a97d14fadd86dda8abd088023c7f9f2dcab2a88
bebatut
parents: 3
diff changeset
38 -AL $advanced.align.align_coverage_long_control
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
39 #end if
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
40
4
ba7e9a012723 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 4a97d14fadd86dda8abd088023c7f9f2dcab2a88
bebatut
parents: 3
diff changeset
41 #if str($advanced.aling.align_coverage_short) != 'None':
ba7e9a012723 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 4a97d14fadd86dda8abd088023c7f9f2dcab2a88
bebatut
parents: 3
diff changeset
42 -aS $advanced.align.align_coverage_short
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
43 #end if
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
44
4
ba7e9a012723 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 4a97d14fadd86dda8abd088023c7f9f2dcab2a88
bebatut
parents: 3
diff changeset
45 #if str($advanced.aling.align_coverage_short_control) != 'None':
ba7e9a012723 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 4a97d14fadd86dda8abd088023c7f9f2dcab2a88
bebatut
parents: 3
diff changeset
46 -AS $advanced.align.align_coverage_short_control
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
47 #end if
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
48
4
ba7e9a012723 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 4a97d14fadd86dda8abd088023c7f9f2dcab2a88
bebatut
parents: 3
diff changeset
49 #if str($advanced.align.align_coverage_min) != 'None':
ba7e9a012723 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 4a97d14fadd86dda8abd088023c7f9f2dcab2a88
bebatut
parents: 3
diff changeset
50 -A $advanced.align.aling_coverage_min
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
51 #end if
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
52 #end if
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
53 #end if
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
54
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
55 #if $print_alignment:
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
56 $print_alignment
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
57 #end if
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
58
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
59 #if $cluster_type:
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
60 $cluster_type
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
61 #end if
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
62
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
63 \$CDHIT_SITE_OPTIONS
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
64
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
65 -T \${GALAXY_SLOTS:-1}
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
66 </template>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
67
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
68 <macro name="common_cdhit_options">
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
69 <conditional name="advanced">
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
70 <param name="settings" type="select" label="Use advanced settings?">
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
71 <option value="no" selected="true">No</option>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
72 <option value="yes">Yes</option>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
73 </param>
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
74
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
75 <when value="no"/>
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
76
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
77 <when value="yes">
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
78 <param name="band_width" type="integer" value="20" optional="true" label="Alignment band width" min="1" help="(-b)"/>
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
79
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
80 <param name="throw_away_len" type="integer" value="10" optional="true" label="Length of throw away sequences" min="1" help="(-l)"/>
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
81
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
82 <param name="description_len" type="integer" value="20" optional="true" label="Length of the description" min="0" help="If set to 0, it takes the fasta defline and stops at first space (-d)"/>
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
83
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
84 <param name="cutoff_diff_len" type="float" value="0.0" optional="true" label="Length difference cutoff" min="0.0" max="1.0" help="If set to 0.9, the shorter sequences need to be at least 90% length of the representative of the cluster (-s)"/>
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
85
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
86 <param name="aa_cutoff_diff_len" type="integer" value="999999" optional="true" label="Length difference cutoff in amino acid" min="0" help="If set to 60, the length difference between the shorter sequences and the representative of the cluster can not be bigger than 60 (-S)"/>
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
87
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
88 <conditional name="align">
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
89 <param name="style" type="select" label="global or local alignments" help="Local sequence identity, calculated as : number of identical amino acids in alignment divided by the length of the alignment. You must set alignment coverage by length or fraction.">
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
90 <option value="global" selected="true">Global</option>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
91 <option value="local" >Local</option>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
92 </param>
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
93
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
94 <when value="global"/>
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
95
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
96 <when value="local">
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
97 <param name="align_coverage_long" type="float" value="0.0" optional="true" label="Alignment coverage for the longer sequence" min="0.0" max="1.0" help="If set to 0.9, the alignment must covers 90% of the sequence (-aL)"/>
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
98
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
99 <param name="align_coverage_long_control" type="integer" value="99999999" optional="true" label="Alignment coverage control for the longer sequence " min="0" help="If set to 60, and the sequence's length 400,then the alignment must be at least 340 (400-60) residues (-AL)"/>
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
100
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
101 <param name="align_coverage_short" type="float" value="0.0" optional="true" label="Alignment coverage for the shorter sequence" min="0.0" max="1.0" help="As for the longer (-aS)"/>
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
102
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
103 <param name="align_coverage_short_control" type="integer" value="99999999" optional="true" label="Alignment coverage control for the shorter sequence" min="0" help="As for the longer (-AS)"/>
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
104
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
105 <param name="align_coverage_min" type="integer" value="0" optional="true" label="Minimal alignment coverage control for the both sequences" min="0" help="Alignment must cover at least this value for both sequences (-A)"/>
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
106 </when>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
107 </conditional>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
108 </when>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
109 </conditional>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
110
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
111 <param name="print_alignment" type="boolean" truevalue="-p 1" falsevalue="" checked="false" label="Print alignment overlap in .clstr file"/>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
112
3
626cd6334dbc planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
bebatut
parents: 2
diff changeset
113 <param name="cluster_type" type="boolean" truevalue="-g 1" falsevalue="" checked="false" label="Slow Cluster" help="In cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast cluster). If set to slow, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode). This won't change the representatives of final clusters (-g)"/>
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
114 </macro>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
115
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
116 </macros>