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genotoul-bioinfo
ng6
Commits
ac42f34d
Commit
ac42f34d
authored
Sep 03, 2012
by
Jerome Mariette
Browse files
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parent
9ea9385a
Changes
16
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ui/nG6/pi1/analyzes/AdaptorcleanerAnalyse.tpl
View file @
ac42f34d
...
...
@@ -22,13 +22,13 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
assign
var
=
"params"
value
=
" "
|
explode
:
$analyse.params
}
<ul>
{
assign
var
=
"score_index"
value
=
$params
|@
array_keys
:
"--score"
}
<li>
{
$llang.AdaptorcleanerAnalyse_minscore
|
replace
:
"###MIN_SCORE###"
:
$params
[
$score_index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.AdaptorcleanerAnalyse_minscore
|
replace
:
"###MIN_SCORE###"
:
$params
[
$score_index
[
0
]+
1
]
}
</li>
{
assign
var
=
"match_index"
value
=
$params
|@
array_keys
:
"--match"
}
<li>
{
$llang.AdaptorcleanerAnalyse_minmatch
|
replace
:
"###MIN_MATCH###"
:
$params
[
$match_index
[
0
]+
1
]
}
</li>
<li>
class="parameter"
{
$llang.AdaptorcleanerAnalyse_minmatch
|
replace
:
"###MIN_MATCH###"
:
$params
[
$match_index
[
0
]+
1
]
}
</li>
{
assign
var
=
"len_index"
value
=
$params
|@
array_keys
:
"--minlen"
}
<li>
{
$llang.AdaptorcleanerAnalyse_minlen
|
replace
:
"###MIN_LEN###"
:
$params
[
$len_index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.AdaptorcleanerAnalyse_minlen
|
replace
:
"###MIN_LEN###"
:
$params
[
$len_index
[
0
]+
1
]
}
</li>
{
if
$analyse_results
[
"all"
][
"default"
][
"adaptor_file"
]
==
""
}
<li>
{
$llang.AdaptorcleanerAnalyse_adaptor
}
<br
/>
<li
class=
"parameter"
>
{
$llang.AdaptorcleanerAnalyse_adaptor
}
<br
/>
{
$isseq
=
false
}
{
foreach
$params
as
$param
}
{
if
$isseq
}
...
...
@@ -43,7 +43,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</li>
{
else
}
{
assign
var
=
"index"
value
=
$params
|@
array_keys
:
"--adaptor"
}
<li>
{
$llang.AdaptorcleanerAnalyse_adaptor
}
<li
class=
"parameter"
>
{
$llang.AdaptorcleanerAnalyse_adaptor
}
<br
/>
<div
class=
"file-display"
>
{
$analyse_results
[
"all"
][
"default"
][
"adaptor_file"
]
}
</div>
</li>
...
...
ui/nG6/pi1/analyzes/BasicAnalyse.tpl
View file @
ac42f34d
...
...
@@ -45,7 +45,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<div
class=
"underline"
>
</div>
{
block
name
=
params_content
}
<ul>
<li>
{
$analyse.params
}
</li>
<li
class=
"parameter"
>
{
$analyse.params
}
</li>
</ul>
{/
block
}
{/
if
}
...
...
ui/nG6/pi1/analyzes/BlastContaminationSearchAnalyse.tpl
View file @
ac42f34d
...
...
@@ -21,8 +21,8 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
block
name
=
params_content
}
{
assign
var
=
"params"
value
=
";"
|
explode
:
$analyse.params
}
<ul>
<li>
{
$params
[
0
]
}
</li>
<li>
{
$params
[
1
]
}
</li>
<li
class=
"parameter"
>
{
$params
[
0
]
}
</li>
<li
class=
"parameter"
>
{
$params
[
1
]
}
</li>
</ul>
{/
block
}
...
...
ui/nG6/pi1/analyzes/CutAdaptAnalyse.tpl
View file @
ac42f34d
...
...
@@ -25,9 +25,9 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
assign
var
=
"max_index"
value
=
$params
|@
array_keys
:
"-M"
}
{
assign
var
=
"adaptor_index"
value
=
$params
|@
array_keys
:
"-a"
}
<ul>
<li>
{
$llang.CutAdaptAnalyse_error_rate
|
replace
:
"###ERROR_RATE###"
:
$params
[
$error_index
[
0
]+
1
]
}
</li>
<li>
{($llang.CutAdaptAnalyse_len|replace:"###MIN_LEN###":$params[$min_index[0]+1])|replace:"###MAX_LEN###":$params[$max_index[0]+1]}
</li>
<li>
{
$llang.CutAdaptAnalyse_adaptors
|
replace
:
"###ADAPTOR_USED###"
:
$params
[
$adaptor_index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.CutAdaptAnalyse_error_rate
|
replace
:
"###ERROR_RATE###"
:
$params
[
$error_index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{($llang.CutAdaptAnalyse_len|replace:"###MIN_LEN###":$params[$min_index[0]+1])|replace:"###MAX_LEN###":$params[$max_index[0]+1]}
</li>
<li
class=
"parameter"
>
{
$llang.CutAdaptAnalyse_adaptors
|
replace
:
"###ADAPTOR_USED###"
:
$params
[
$adaptor_index
[
0
]+
1
]
}
</li>
</ul>
{/
block
}
...
...
ui/nG6/pi1/analyzes/FastqIlluminaFilterAnalyse.tpl
View file @
ac42f34d
...
...
@@ -23,9 +23,9 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
assign
var
=
"filter_index"
value
=
$params
|@
array_keys
:
"--keep"
}
<ul>
{
if
$params
[
$filter_index
[
0
]+
1
]
==
"N"
}
<li>
{
$llang.FastqIlluminaFilterAnalyse_Nparams
}
</li>
<li
class=
"parameter"
>
{
$llang.FastqIlluminaFilterAnalyse_Nparams
}
</li>
{
else
}
<li>
{
$llang.FastqIlluminaFilterAnalyse_Yparams
}
</li>
<li
class=
"parameter"
>
{
$llang.FastqIlluminaFilterAnalyse_Yparams
}
</li>
{/
if
}
</ul>
{/
block
}
...
...
ui/nG6/pi1/analyzes/FlashAnalyse.tpl
View file @
ac42f34d
...
...
@@ -26,19 +26,19 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<ul>
{
if
in_array
(
"-m"
,
$params
)
}
{
assign
var
=
"mindex"
value
=
$params
|@
array_keys
:
"-m"
}
<li>
{
$llang.FlashAnalyse_min_overlap
|
replace
:
"###MINOVERLAP###"
:
$params
[
$mindex
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.FlashAnalyse_min_overlap
|
replace
:
"###MINOVERLAP###"
:
$params
[
$mindex
[
0
]+
1
]
}
</li>
{/
if
}
{
if
in_array
(
"-M"
,
$params
)
}
{
assign
var
=
"m2index"
value
=
$params
|@
array_keys
:
"-M"
}
<li>
{
$llang.FlashAnalyse_max_overlap
|
replace
:
"###MAXOVERLAP###"
:
$params
[
$m2index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.FlashAnalyse_max_overlap
|
replace
:
"###MAXOVERLAP###"
:
$params
[
$m2index
[
0
]+
1
]
}
</li>
{/
if
}
{
if
in_array
(
"-x"
,
$params
)
}
{
assign
var
=
"xindex"
value
=
$params
|@
array_keys
:
"-x"
}
<li>
{
$llang.FlashAnalyse_mismatch_ratio
|
replace
:
"###MISMATCHRATIO###"
:
$params
[
$xindex
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.FlashAnalyse_mismatch_ratio
|
replace
:
"###MISMATCHRATIO###"
:
$params
[
$xindex
[
0
]+
1
]
}
</li>
{/
if
}
{
if
in_array
(
"-p"
,
$params
)
}
{
assign
var
=
"pindex"
value
=
$params
|@
array_keys
:
"-p"
}
<li>
{
$llang.FlashAnalyse_phred_offset
|
replace
:
"###PHREDOFFSET###"
:
$params
[
$pindex
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.FlashAnalyse_phred_offset
|
replace
:
"###PHREDOFFSET###"
:
$params
[
$pindex
[
0
]+
1
]
}
</li>
{/
if
}
</ul>
{/
block
}
...
...
ui/nG6/pi1/analyzes/MothurAlignAnalyse.tpl
View file @
ac42f34d
...
...
@@ -22,7 +22,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
assign
var
=
"params"
value
=
";"
|
explode
:
$analyse.params
}
<ul>
{
foreach
from
=
$params
item
=
param
}
<li
>
{
$par
am
}
</li>
<li
class=
"parameter"
am
}</
li
>
{/
foreach
}
</ul>
{/
block
}
...
...
ui/nG6/pi1/analyzes/MothurClassifyAnalyse.tpl
View file @
ac42f34d
...
...
@@ -22,7 +22,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
assign
var
=
"params"
value
=
";"
|
explode
:
$analyse.params
}
<ul>
{
foreach
from
=
$params
item
=
param
}
<li>
{
$param
}
</li>
<li
class=
"parameter"
>
{
$param
}
</li>
{/
foreach
}
</ul>
{/
block
}
...
...
ui/nG6/pi1/analyzes/MothurOTUAnalyse.tpl
View file @
ac42f34d
...
...
@@ -22,7 +22,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
assign
var
=
"params"
value
=
";"
|
explode
:
$analyse.params
}
<ul>
{
foreach
from
=
$params
item
=
param
}
<li>
{
$param
}
</li>
<li
class=
"parameter"
>
{
$param
}
</li>
{/
foreach
}
</ul>
{/
block
}
...
...
ui/nG6/pi1/analyzes/PyrocleanerAnalyse.tpl
View file @
ac42f34d
...
...
@@ -23,16 +23,16 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<ul>
{
if
in_array
(
"--clean-length-std"
,
$params
)
}
{
assign
var
=
"index"
value
=
$params
|@
array_keys
:
"--std"
}
<li>
{
$llang.PyrocleanerAnalyse_length_std_param
|
replace
:
"###STD###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.PyrocleanerAnalyse_length_std_param
|
replace
:
"###STD###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
{/
if
}
{
if
in_array
(
"--clean-length-win"
,
$params
)
}
{
assign
var
=
"min_index"
value
=
$params
|@
array_keys
:
"--min"
}
{
assign
var
=
"max_index"
value
=
$params
|@
array_keys
:
"--max"
}
<li>
{($llang.PyrocleanerAnalyse_length_win_param|replace:"###MIN_SIZE###":$params[$min_index[0]+1])|replace:"###MAX_SIZE###":$params[$max_index[0]+1]}
</li>
<li
class=
"parameter"
>
{($llang.PyrocleanerAnalyse_length_win_param|replace:"###MIN_SIZE###":$params[$min_index[0]+1])|replace:"###MAX_SIZE###":$params[$max_index[0]+1]}
</li>
{/
if
}
{
if
in_array
(
"--clean-ns"
,
$params
)
}
{
assign
var
=
"index"
value
=
$params
|@
array_keys
:
"--ns_percent"
}
<li>
{
$llang.PyrocleanerAnalyse_ns_param
|
replace
:
"###NS_PERCENT###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.PyrocleanerAnalyse_ns_param
|
replace
:
"###NS_PERCENT###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
{/
if
}
{
if
in_array
(
"--clean-complexity-win"
,
$params
)
}
{
assign
var
=
"win_index"
value
=
$params
|@
array_keys
:
"--window"
}
...
...
@@ -42,23 +42,23 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/
if
}
{
if
in_array
(
"--clean-complexity-full"
,
$params
)
}
{
assign
var
=
"index"
value
=
$params
|@
array_keys
:
"--complexity"
}
<li>
{
$llang.PyrocleanerAnalyse_complexity_full_param
|
replace
:
"###COMPLEXIT_RATIO###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.PyrocleanerAnalyse_complexity_full_param
|
replace
:
"###COMPLEXIT_RATIO###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
{/
if
}
{
if
in_array
(
"--clean-quality"
,
$params
)
}
{
assign
var
=
"index"
value
=
$params
|@
array_keys
:
"--quality-threshold"
}
<li>
{
$llang.PyrocleanerAnalyse_qual_param
|
replace
:
"###MIN_QUAL###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.PyrocleanerAnalyse_qual_param
|
replace
:
"###MIN_QUAL###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
{/
if
}
{
if
in_array
(
"--clean-duplicated-reads"
,
$params
)
AND
in_array
(
"--aggressive"
,
$params
)
}
{
assign
var
=
"index"
value
=
$params
|@
array_keys
:
"--duplication_limit"
}
<li>
{
$llang.PyrocleanerAnalyse_duplication_aggressive_param
|
replace
:
"###SIZE_LIMIT###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.PyrocleanerAnalyse_duplication_aggressive_param
|
replace
:
"###SIZE_LIMIT###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
{
elseif
in_array
(
"--clean-duplicated-reads"
,
$params
)
}
{
assign
var
=
"index"
value
=
$params
|@
array_keys
:
"--duplication_limit"
}
<li>
{
$llang.PyrocleanerAnalyse_duplication_param
|
replace
:
"###SIZE_LIMIT###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.PyrocleanerAnalyse_duplication_param
|
replace
:
"###SIZE_LIMIT###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
{/
if
}
{
if
in_array
(
"--clean-pairends"
,
$params
)
}
{
assign
var
=
"border_index"
value
=
$params
|@
array_keys
:
"--border-limit"
}
{
assign
var
=
"match_index"
value
=
$params
|@
array_keys
:
"--missmatch"
}
<li>
{($llang.PyrocleanerAnalyse_pairend_param|replace:"###BORDER_LIMIT###":$params[$border_index[0]+1])|replace:"###MIN_MATCHES###":$params[$match_index[0]+1]}
</li>
<li
class=
"parameter"
>
{($llang.PyrocleanerAnalyse_pairend_param|replace:"###BORDER_LIMIT###":$params[$border_index[0]+1])|replace:"###MIN_MATCHES###":$params[$match_index[0]+1]}
</li>
{/
if
}
</ul>
{/
block
}
...
...
ui/nG6/pi1/analyzes/RunAssemblyAnalyse.tpl
View file @
ac42f34d
...
...
@@ -21,7 +21,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
block
name
=
params_content
}
{
assign
var
=
"params"
value
=
" "
|
explode
:
$analyse.params
}
<ul>
<li>
{
$analyse.params
}
</li>
<li
class=
"parameter"
>
{
$analyse.params
}
</li>
</ul>
{/
block
}
...
...
ui/nG6/pi1/analyzes/S16CleanerAnalyse.tpl
View file @
ac42f34d
...
...
@@ -26,11 +26,11 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{* Filter on min number of matches *}
{
if
in_array
(
"--fwd-minmatch"
,
$params
)
}
{
assign
var
=
"min_fwd_index"
value
=
$params
|@
array_keys
:
"--fwd-minmatch"
}
<li>
{($llang.S16CleanerAnalyse_fwd_param|replace:"###FWD###":$params[$fwd_index[0]+1])|replace:"###MIN_FWD###":$params[$min_fwd_index[0]+1]}
</li>
<li
class=
"parameter"
>
{($llang.S16CleanerAnalyse_fwd_param|replace:"###FWD###":$params[$fwd_index[0]+1])|replace:"###MIN_FWD###":$params[$min_fwd_index[0]+1]}
</li>
{* Filter on max number of errors *}
{
else
}
{
assign
var
=
"max_fwd_index"
value
=
$params
|@
array_keys
:
"--fwd-maxerror"
}
<li>
{($llang.S16CleanerAnalyse_fwd_err_param|replace:"###FWD###":$params[$fwd_index[0]+1])|replace:"###MAX_FWD###":$params[$max_fwd_index[0]+1]}
</li>
<li
class=
"parameter"
>
{($llang.S16CleanerAnalyse_fwd_err_param|replace:"###FWD###":$params[$fwd_index[0]+1])|replace:"###MAX_FWD###":$params[$max_fwd_index[0]+1]}
</li>
{/
if
}
{/
if
}
{
if
in_array
(
"--reverse"
,
$params
)
}
...
...
@@ -38,29 +38,29 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{* Filter on min number of matches *}
{
if
in_array
(
"--rvrs-minmatch"
,
$params
)
}
{
assign
var
=
"min_rvrs_index"
value
=
$params
|@
array_keys
:
"--rvrs-minmatch"
}
<li>
{($llang.S16CleanerAnalyse_rvrs_param|replace:"###RVRS###":$params[$rvrs_index[0]+1])|replace:"###MIN_RVRS###":$params[$min_rvrs_index[0]+1]}
</li>
<li
class=
"parameter"
>
{($llang.S16CleanerAnalyse_rvrs_param|replace:"###RVRS###":$params[$rvrs_index[0]+1])|replace:"###MIN_RVRS###":$params[$min_rvrs_index[0]+1]}
</li>
{* Filter on max number of errors *}
{
else
}
{
assign
var
=
"max_rvrs_index"
value
=
$params
|@
array_keys
:
"--rvrs-maxerror"
}
<li>
{($llang.S16CleanerAnalyse_rvrs_err_param|replace:"###RVRS###":$params[$rvrs_index[0]+1])|replace:"###MAX_RVRS###":$params[$max_rvrs_index[0]+1]}
</li>
<li
class=
"parameter"
>
{($llang.S16CleanerAnalyse_rvrs_err_param|replace:"###RVRS###":$params[$rvrs_index[0]+1])|replace:"###MAX_RVRS###":$params[$max_rvrs_index[0]+1]}
</li>
{/
if
}
{/
if
}
{
if
in_array
(
"--clean-length"
,
$params
)
}
{
assign
var
=
"min_index"
value
=
$params
|@
array_keys
:
"--min-length"
}
{
assign
var
=
"max_index"
value
=
$params
|@
array_keys
:
"--max-length"
}
<li>
{($llang.S16CleanerAnalyse_length_win_param|replace:"###MIN_SIZE###":$params[$min_index[0]+1])|replace:"###MAX_SIZE###":$params[$max_index[0]+1]}
</li>
<li
class=
"parameter"
>
{($llang.S16CleanerAnalyse_length_win_param|replace:"###MIN_SIZE###":$params[$min_index[0]+1])|replace:"###MAX_SIZE###":$params[$max_index[0]+1]}
</li>
{/
if
}
{
if
in_array
(
"--clean-ns"
,
$params
)
}
{
assign
var
=
"index"
value
=
$params
|@
array_keys
:
"--ns-percent"
}
<li>
{
$llang.S16CleanerAnalyse_ns_param
|
replace
:
"###NS_PERCENT###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.S16CleanerAnalyse_ns_param
|
replace
:
"###NS_PERCENT###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
{/
if
}
{
if
in_array
(
"--clean-homopolymers"
,
$params
)
}
{
assign
var
=
"index"
value
=
$params
|@
array_keys
:
"--homopolymers-length"
}
<li>
{
$llang.S16CleanerAnalyse_homopolymer_param
|
replace
:
"###HOMO_SIZE###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.S16CleanerAnalyse_homopolymer_param
|
replace
:
"###HOMO_SIZE###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
{/
if
}
{
if
in_array
(
"--clean-full-length"
,
$params
)
}
{
assign
var
=
"index"
value
=
$params
|@
array_keys
:
"--full-length-min-size"
}
<li>
{
$llang.S16CleanerAnalyse_full_size_param
|
replace
:
"###FULL_MIN_SIZE###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.S16CleanerAnalyse_full_size_param
|
replace
:
"###FULL_MIN_SIZE###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
{/
if
}
</ul>
{/
block
}
...
...
ui/nG6/pi1/analyzes/SFFFileAnalyse.tpl
View file @
ac42f34d
...
...
@@ -25,12 +25,12 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
assign
var
=
"sample"
value
=
$sample
}
{/
foreach
}
<ul>
<li>
{
$analyse.params
}
</li>
<li>
{($llang.SFFFileAnalyse_file_content|replace:"###FILE_NAME###":"
<strong>
###FILE_NAME###
</strong>
")|replace:"###FILE_NAME###":$params[$index[0]+1]}
<li
class=
"parameter"
>
{
$analyse.params
}
</li>
<li
class=
"parameter"
>
{($llang.SFFFileAnalyse_file_content|replace:"###FILE_NAME###":"
<strong>
###FILE_NAME###
</strong>
")|replace:"###FILE_NAME###":$params[$index[0]+1]}
<br
/>
<div
class=
"file-display"
>
{
$analyse_results
[
$sample
][
"default"
][
"config_file"
]
}
</div>
<i>
with: mid = "
{
$llang.Analyse_sample
}
", "fwd_seq", nb_missmatch, "rvrs_seq";
</i>
</li>
</li
class="parameter"
>
</ul>
{/
block
}
...
...
ui/nG6/pi1/analyzes/SmartkitcleanerAnalyse.tpl
View file @
ac42f34d
...
...
@@ -24,31 +24,31 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
if
in_array
(
"--clean-length"
,
$params
)
}
{
assign
var
=
"min_index"
value
=
$params
|@
array_keys
:
"--min-length"
}
{
assign
var
=
"max_index"
value
=
$params
|@
array_keys
:
"--max-length"
}
<li>
{($llang.SmartkitcleanerAnalyse_length_param|replace:"###MIN_SIZE###":$params[$min_index[0]+1])|replace:"###MAX_SIZE###":$params[$max_index[0]+1]}
</li>
<li
class=
"parameter"
>
{($llang.SmartkitcleanerAnalyse_length_param|replace:"###MIN_SIZE###":$params[$min_index[0]+1])|replace:"###MAX_SIZE###":$params[$max_index[0]+1]}
</li>
{/
if
}
{
if
in_array
(
"--clean-ns"
,
$params
)
}
{
assign
var
=
"ns_index"
value
=
$params
|@
array_keys
:
"--ns-percent"
}
<li>
{
$llang.SmartkitcleanerAnalyse_ns_param
|
replace
:
"###NS_PERCENT###"
:
$params
[
$ns_index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.SmartkitcleanerAnalyse_ns_param
|
replace
:
"###NS_PERCENT###"
:
$params
[
$ns_index
[
0
]+
1
]
}
</li>
{/
if
}
{
if
in_array
(
"--clean-complexity-win"
,
$params
)
}
{
assign
var
=
"win_index"
value
=
$params
|@
array_keys
:
"--window"
}
{
assign
var
=
"step_index"
value
=
$params
|@
array_keys
:
"--step"
}
{
assign
var
=
"ratio_index"
value
=
$params
|@
array_keys
:
"--complexity"
}
<li>
{(($llang.SmartkitcleanerAnalyse_complexity_win_param|replace:"###WINDOW_SIZE###":$params[$win_index[0]+1])|replace:"###STEP_SIZE###":$params[$step_index[0]+1])|replace:"###COMPLEXIT_RATIO###":$params[$ratio_index[0]+1]}
</li>
<li
class=
"parameter"
>
{(($llang.SmartkitcleanerAnalyse_complexity_win_param|replace:"###WINDOW_SIZE###":$params[$win_index[0]+1])|replace:"###STEP_SIZE###":$params[$step_index[0]+1])|replace:"###COMPLEXIT_RATIO###":$params[$ratio_index[0]+1]}
</li>
{/
if
}
{
if
in_array
(
"--clean-complexity-full"
,
$params
)
}
{
assign
var
=
"index"
value
=
$params
|@
array_keys
:
"--complexity"
}
<li>
{
$llang.SmartkitcleanerAnalyse_complexity_full_param
|
replace
:
"###COMPLEXIT_RATIO###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.SmartkitcleanerAnalyse_complexity_full_param
|
replace
:
"###COMPLEXIT_RATIO###"
:
$params
[
$index
[
0
]+
1
]
}
</li>
{/
if
}
{
assign
var
=
"seq1_index"
value
=
$params
|@
array_keys
:
"--primer1"
}
{
assign
var
=
"match1_index"
value
=
$params
|@
array_keys
:
"--primer1-minmatch"
}
{
assign
var
=
"score1_index"
value
=
$params
|@
array_keys
:
"--primer1-score"
}
{
assign
var
=
"undef1_index"
value
=
$params
|@
array_keys
:
"--primer1-undef"
}
<li>
{((($llang.SmartkitcleanerAnalyse_adapt1|replace:"###ADAPT1_SEQ###":$params[$seq1_index[0]+1])|replace:"###ADAPT1_MATCHES###":$params[$match1_index[0]+1])|replace:"###ADAPT1_SCORE###":$params[$score1_index[0]+1])|replace:"###ADAPT1_UNDEF###":$params[$undef1_index[0]+1]}
</li>
<li
class=
"parameter"
>
{((($llang.SmartkitcleanerAnalyse_adapt1|replace:"###ADAPT1_SEQ###":$params[$seq1_index[0]+1])|replace:"###ADAPT1_MATCHES###":$params[$match1_index[0]+1])|replace:"###ADAPT1_SCORE###":$params[$score1_index[0]+1])|replace:"###ADAPT1_UNDEF###":$params[$undef1_index[0]+1]}
</li>
{
assign
var
=
"seq2_index"
value
=
$params
|@
array_keys
:
"--primer2"
}
{
assign
var
=
"match2_index"
value
=
$params
|@
array_keys
:
"--primer2-minmatch"
}
{
assign
var
=
"score2_index"
value
=
$params
|@
array_keys
:
"--primer2-score"
}
<li>
{(($llang.SmartkitcleanerAnalyse_adapt2|replace:"###ADAPT2_SEQ###":$params[$seq2_index[0]+1])|replace:"###ADAPT2_MATCHES###":$params[$match2_index[0]+1])|replace:"###ADAPT2_SCORE###":$params[$score2_index[0]+1]}
</li>
<li
class=
"parameter"
>
{(($llang.SmartkitcleanerAnalyse_adapt2|replace:"###ADAPT2_SEQ###":$params[$seq2_index[0]+1])|replace:"###ADAPT2_MATCHES###":$params[$match2_index[0]+1])|replace:"###ADAPT2_SCORE###":$params[$score2_index[0]+1]}
</li>
</ul>
{/
block
}
...
...
ui/nG6/pi1/analyzes/SplitbcAnalyse.tpl
View file @
ac42f34d
...
...
@@ -25,18 +25,18 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/
foreach
}
<ul>
{
if
in_array
(
"--trim"
,
$params
)
}
<li>
{
$llang.SplitbcAnalyse_trim_param
}
</li>
<li
class=
"parameter"
>
{
$llang.SplitbcAnalyse_trim_param
}
</li>
{/
if
}
{
if
in_array
(
"--mismatches"
,
$params
)
}
{
assign
var
=
"mindex"
value
=
$params
|@
array_keys
:
"--mismatches"
}
<li>
{
$llang.SplitbcAnalyse_nb_missmatch
|
replace
:
"###MISSMATCH###"
:
$params
[
$mindex
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.SplitbcAnalyse_nb_missmatch
|
replace
:
"###MISSMATCH###"
:
$params
[
$mindex
[
0
]+
1
]
}
</li>
{/
if
}
{
if
in_array
(
"--partial"
,
$params
)
}
{
assign
var
=
"pindex"
value
=
$params
|@
array_keys
:
"--partial"
}
<li>
{
$llang.SplitbcAnalyse_nb_partial
|
replace
:
"###PARTIAL###"
:
$params
[
$pindex
[
0
]+
1
]
}
</li>
<li
class=
"parameter"
>
{
$llang.SplitbcAnalyse_nb_partial
|
replace
:
"###PARTIAL###"
:
$params
[
$pindex
[
0
]+
1
]
}
</li>
{/
if
}
{
assign
var
=
"index"
value
=
$params
|@
array_keys
:
"--bcfile"
}
<li>
{
$llang.SplitbcAnalyse_barecode_used
}
<li
class=
"parameter"
>
{
$llang.SplitbcAnalyse_barecode_used
}
<br
/>
<div
class=
"file-display"
>
{
$analyse_results
[
"barecode_file"
][
"default"
][
"barecode_file"
]
}
</div>
</li>
...
...
ui/nG6/res/css/tx_nG6.css
View file @
ac42f34d
...
...
@@ -174,6 +174,7 @@ table.tx-nG6-pi1-listrow tr.tx-nG6-pi1-listrowlast{
}
table
.tx-nG6-pi1-listrow
td
{
border-bottom
:
1px
solid
#ddd
;
}
ul
li
.filelist
{
list-style
:
none
;
margin-left
:
10px
;
padding-left
:
17px
;
background
:
url(../img/ico-fleche.png)
left
4px
no-repeat
;
}
ul
li
.parameter
{
list-style
:
none
;
margin-left
:
10px
;
padding-left
:
17px
;
background
:
url(../img/ico-fleche.png)
left
4px
no-repeat
;
}
.tx-nG6-pi1-hidden
{
color
:
#9a9a9a
;
}
.tx-nG6-pi1-hidden
a
{
color
:
#aacbfb
;
}
.tx-nG6-pi1-help
{
...
...
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