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genotoul-bioinfo
ng6
Commits
1805799a
Commit
1805799a
authored
Aug 27, 2014
by
Penom Nom
Browse files
command line parameters edition
parent
f89d3f82
Changes
6
Hide whitespace changes
Inline
Side-by-side
ui/nG6/pi1/analyzes/AnalysisTemplate.tpl
View file @
1805799a
...
...
@@ -53,6 +53,22 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<li
class=
"parameter"
>
{
$analyse.params
}
</li>
</ul>
{/
block
}
{
block
name
=
command_line_content
}
{
if
$is_project_admin
}
<br/>
<br/>
<div
class=
"editable-block"
>
<span
class=
"editable-block-head label label-info"
>
Command
</span>
<i>
{
$analyse.software
}
</i>
<span
class=
"editable editable-block-content"
id=
"editable-command-line"
data-pk=
"
{
$analyze_id
}
"
data-url=
"index.php?eID=tx_nG6&type=update_db_field&table=tx_nG6_analyze&field=params"
data-type=
"textarea"
>
{
$analyse.params
}
</span>
</div>
{/
if
}
{/
block
}
{/
block
}
</div>
{/
if
}
...
...
ui/nG6/pi1/analyzes/FastQC.tpl
View file @
1805799a
...
...
@@ -17,7 +17,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
extends
file
=
'AnalysisTemplate.tpl'
}
{
block
name
=
params
}
{
block
name
=
params
_content
}
{
assign
var
=
"params"
value
=
" "
|
explode
:
$analyse.params
}
<ul>
{
if
in_array
(
"--casava"
,
$params
)
}
...
...
ui/nG6/pi1/class.tx_nG6_pi1.php
View file @
1805799a
...
...
@@ -338,6 +338,7 @@ class tx_nG6_pi1 extends tslib_pibase {
$analysis_size
=
tx_nG6_db
::
get_analysis_size
(
$this
->
piVars
[
'analyze_id'
]);
$smarty
->
assign
(
'analyse_size'
,
tx_nG6_utils
::
get_octet_string_representation
(
$analysis_size
));
$smarty
->
assign
(
'data_folder'
,
$this
->
conf
[
"data"
]);
$smarty
->
assign
(
'analyze_id'
,
$this
->
piVars
[
'analyze_id'
]);
// Then select analyse results
$results
=
tx_nG6_db
::
select_analyse_results
(
$this
->
piVars
[
'analyze_id'
]);
...
...
ui/nG6/res/css/tx_nG6.css
View file @
1805799a
...
...
@@ -235,8 +235,29 @@ td.editable:hover {
cursor
:
text
;
background-color
:
#f0f2f2
!important
;
}
span
.editable
:hover
{
/*border-bottom: 1px dashed #52A8EC;*/
.editable-block
{
position
:
relative
;
padding
:
10px
5px
10px
5px
;
background-color
:
white
;
border
:
1px
solid
lightgrey
;
border-radius
:
5px
;
font-weight
:
bold
;
}
.editable-block
:hover
{
cursor
:
text
;
border
:
1px
dashed
#52A8EC
;
background-color
:
#f0f2f2
!important
;
}
.editable-block-head
{
position
:
absolute
;
top
:
-15px
;
}
.editable-block-content
:hover
{
cursor
:
text
;
background-color
:
#f0f2f2
!important
;
}
/* tx-nG-pi6 plugin style */
...
...
@@ -294,4 +315,4 @@ div#chart_options{
fill
:
none
;
stroke
:
#ccc
;
stroke-width
:
1.5px
;
}
\ No newline at end of file
}
ui/nG6/res/js/tx_nG6_pi1_analysis.js
View file @
1805799a
...
...
@@ -54,6 +54,15 @@ function modal_height(substract, min) {
}
$
(
function
()
{
// Grab relevant info from URL fragment
var
params
=
simpleQueryParams
(
location
.
href
),
active_tab
=
params
[
"
active_tab
"
];
if
(
active_tab
)
{
$
(
'
#myTab a[href="#
'
+
active_tab
+
'
"]
'
).
tab
(
'
show
'
);
}
$
(
"
.file-display
"
).
each
(
function
(
i
){
$
(
this
).
attr
(
"
id
"
,
"
file_display_
"
+
i
);
var
id
=
"
file_display_
"
+
i
;
...
...
@@ -181,6 +190,28 @@ $(function () {
}
});
// init editable
$
(
'
.editable-block .editable-block-content
'
).
editable
({
toggle
:
'
manual
'
});
$
(
'
.editable-block
'
).
click
(
function
(
e
){
e
.
stopPropagation
();
$
(
this
).
children
(
'
.editable-block-content
'
).
editable
(
'
option
'
,
'
container
'
,
'
body
'
);
$
(
this
).
children
(
'
.editable-block-content
'
).
editable
(
'
option
'
,
'
success
'
,
function
()
{
location
.
assign
(
location
.
href
+
"
&active_tab=parameters
"
);
});
$
(
this
).
children
(
'
.editable-block-content
'
).
editable
(
'
show
'
);
});
$
(
'
.editable-block-content
'
).
click
(
function
(
e
){
e
.
stopPropagation
();
$
(
this
).
editable
(
'
option
'
,
'
success
'
,
function
()
{
location
.
assign
(
location
.
href
+
"
&active_tab=parameters
"
);
});
$
(
this
).
editable
(
'
option
'
,
'
container
'
,
'
body
'
);
$
(
this
).
editable
(
'
show
'
);
})
// Add numeric with white space in sort
jQuery
.
extend
(
jQuery
.
fn
.
dataTableExt
.
oSort
,
{
"
numeric-pre
"
:
function
(
a
)
{
...
...
@@ -195,5 +226,5 @@ $(function () {
"
numeric-desc
"
:
function
(
a
,
b
)
{
return
b
-
a
;
}
});
});
});
workflows/components/splitbc.py
View file @
1805799a
...
...
@@ -105,7 +105,7 @@ class Splitbc (Analysis):
def
define_analysis
(
self
):
self
.
name
=
"Demultiplexing"
self
.
description
=
"demultiplexing samples"
self
.
software
=
"Splitbc"
self
.
software
=
os
.
path
.
basename
(
self
.
get_exec_path
(
"splitbc.pl"
))
self
.
options
=
[
"--bcfile"
,
self
.
barcode_file
]
if
self
.
bol
:
...
...
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