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comparison cdhit_macros.xml @ 12:b1bf31be0d3c default tip

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Fix cheetah tests of whether optional arguments are set
author Jim Johnson <jj@umn.edu>
date Thu, 29 Oct 2015 10:09:02 -0500
parents 75fde37f69e5
children
comparison
equal deleted inserted replaced
11:75fde37f69e5 12:b1bf31be0d3c
2 <template name="common_cdhit_options"> 2 <template name="common_cdhit_options">
3 <!-- start common cdhit options --> 3 <!-- start common cdhit options -->
4 4
5 <!-- start adv. settings --> 5 <!-- start adv. settings -->
6 #if $advanced.settings == 'yes': 6 #if $advanced.settings == 'yes':
7 #if $advanced.band_width: 7 #if str($advanced.band_width) != 'None':
8 -b $advanced.band_width 8 -b $advanced.band_width
9 #end if 9 #end if
10 #if $advanced.throw_away_len: 10 #if str($advanced.throw_away_len) != 'None':
11 -l $advanced.throw_away_len 11 -l $advanced.throw_away_len
12 #end if 12 #end if
13 #if $advanced.description_len: 13 #if str($advanced.description_len) != 'None':
14 -d $advanced.description_len 14 -d $advanced.description_len
15 #end if 15 #end if
16 #if $advanced.cutoff_diff_len: 16 #if str($advanced.cutoff_diff_len) != 'None':
17 -s $advanced.cutoff_diff_len 17 -s $advanced.cutoff_diff_len
18 #end if 18 #end if
19 #if $advanced.aa_cutoff_diff_len: 19 #if str($advanced.aa_cutoff_diff_len) != 'None':
20 -S $advanced.aa_cutoff_diff_len 20 -S $advanced.aa_cutoff_diff_len
21 #end if 21 #end if
22 #if $advanced.align.style == 'local': 22 #if $advanced.align.style == 'local':
23 -G 0 23 -G 0
24 #if $advance.align.align_coverage_long: 24 #if str($advance.align.align_coverage_long) != 'None':
25 -aL $advance.align.align_coverage_long 25 -aL $advance.align.align_coverage_long
26 #end if 26 #end if
27 #if $advance.align.aa_align_coverage_long: 27 #if str($advance.align.aa_align_coverage_long) != 'None':
28 -AL $advance.align.aa_align_coverage_long 28 -AL $advance.align.aa_align_coverage_long
29 #end if 29 #end if
30 #if $advance.aling.align_coverage_short: 30 #if str($advance.aling.align_coverage_short) != 'None':
31 -aS $advance.align.align_coverage_short 31 -aS $advance.align.align_coverage_short
32 #end if 32 #end if
33 #if $advance.aling.aa_align_coverage_short: 33 #if str($advance.aling.aa_align_coverage_short) != 'None':
34 -AS $advance.align.aa_align_coverage_short 34 -AS $advance.align.aa_align_coverage_short
35 #end if 35 #end if
36 #if $advance.align.align_coverage_min: 36 #if str($advance.align.align_coverage_min) != 'None':
37 -A $advance.align.aling_coverage_min 37 -A $advance.align.aling_coverage_min
38 #end if 38 #end if
39 #end if 39 #end if
40 #end if 40 #end if
41 <!-- end adv. settings --> 41 <!-- end adv. settings -->