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genotoul-bioinfo
jflow
Commits
15c74f57
Commit
15c74f57
authored
Mar 19, 2015
by
Philippe Bardou
Browse files
Alert div
Handsonetable width 695px!
parent
ff44db24
Changes
4
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Inline
Side-by-side
docs/jflow-core-component.html
View file @
15c74f57
...
...
@@ -672,8 +672,10 @@ class MyComponent (Component):
<h3>
add_output_file_endswith()
</h3>
<span
class=
"glyphicon glyphicon-exclamation-sign"
aria-hidden=
"true"
></span>
This method should only be used with components producing unknown number of outputs (like some demultiplexing tools).
<div
class=
"alert alert-info"
role=
"alert"
>
<span
class=
"glyphicon glyphicon-exclamation-sign"
aria-hidden=
"true"
></span>
This method should only be used with components producing unknown number of outputs (like some demultiplexing tools).
</div>
<h4>
Example
</h4>
<p>
...
...
@@ -791,9 +793,10 @@ class MyComponent (Component):
<h3>
add_output_file_pattern()
</h3>
<span
class=
"glyphicon glyphicon-exclamation-sign"
aria-hidden=
"true"
></span>
This method should only be used with components producing unknown number of outputs (like some demultiplexing tools).
<div
class=
"alert alert-info"
role=
"alert"
>
<span
class=
"glyphicon glyphicon-exclamation-sign"
aria-hidden=
"true"
></span>
This method should only be used with components producing unknown number of outputs (like some demultiplexing tools).
</div>
<h4>
Example
</h4>
<p>
...
...
@@ -851,13 +854,14 @@ class MyComponent (Component):
<code>
ShellFunction
</code>
and
<code>
PythonFunction
</code>
and two main abstractions:
<code>
Map
</code>
and
<code>
MultiMap
</code>
.
</p>
<
p
>
<
div
class=
"alert alert-info"
role=
"alert"
>
<span
class=
"glyphicon glyphicon-exclamation-sign"
aria-hidden=
"true"
></span>
Overloading
<code>
process()
</code>
can be omitted. Jflow offers, for components with easy command lines,
an automatic built of the
<code>
process()
</code>
method.
In this case, options
<code>
argpos
</code>
and
<code>
cmd_format
</code>
must be provided by the developper for each parameter.
Also, two other methods of
<code>
jflow.component.Component
</code>
must be overloaded.
<code>
get_command()
</code>
, which must returns
the execution path and
<code>
get_abstraction()
</code>
which returns the abstraction name to use.
</p>
In this case, options
<code>
argpos
</code>
and
<code>
cmd_format
</code>
must be provided by the developper for each parameter.
Also, two other methods of
<code>
jflow.component.Component
</code>
must be overloaded.
<code>
get_command()
</code>
, which must returns
the execution path and
<code>
get_abstraction()
</code>
which returns the abstraction name to use.
</div>
<div
id=
"functions"
class=
"subgroup"
>
...
...
@@ -1304,12 +1308,15 @@ fastq2fasta.py --input splC.fastq --fasta splC.fasta --qual splC.qual</code></pr
<p>
The method
<code>
build_component()
</code>
must be used to return the new component type.The newly created component type must
have a definition of
<code>
define_parameters()
</code>
. If the
<code>
process()
</code>
method is not redefined, the developper has to overload
<code>
get_abstraction()
</code>
and
<code>
get_command()
</code>
. See
<a
href=
"#process"
>
process
</a>
for more details.
</p>
<p>
<span
class=
"glyphicon glyphicon-exclamation-sign"
aria-hidden=
"true"
></span>
Jflow provides
<code>
extparsers.mobyle.MobyleParser
</code>
class as an example to integrate new external component parsers. Adding this class
the developper can add mobyle components, defined by an XML file, by copying the XML definition of the component in any jflow
<code>
components
</code>
packages.
</p>
<p>
<div
class=
"alert alert-info"
role=
"alert"
>
<span
class=
"glyphicon glyphicon-exclamation-sign"
aria-hidden=
"true"
></span>
Jflow provides
<code>
extparsers.mobyle.MobyleParser
</code>
class as an example to integrate new external component parsers. Adding this class
the developper can add mobyle components, defined by an XML file, by copying the XML definition of the component in any jflow
<code>
components
</code>
packages.
</div>
<h3>
parse()
</h3>
<p>
The
<code>
parse()
</code>
function is the only function to implement. This function will be called by jflow
and will be executed on any file present in jflow
<code>
components
</code>
packages not recognized as an internal
...
...
docs/jflow-core-workflow.html
View file @
15c74f57
...
...
@@ -170,9 +170,10 @@ class MyWorkflow (Workflow):
arguments:
<code>
name
</code>
and
<code>
help
</code>
. The other arguments are optional and can be given to the method by using their
keywords.
</p>
<span
class=
"glyphicon glyphicon-exclamation-sign"
aria-hidden=
"true"
></span>
The operator
<code>
is
</code>
is not supported to evaluate a parameter, the operator
<code>
==
</code>
must be prefered.
<div
class=
"alert alert-info"
role=
"alert"
>
<span
class=
"glyphicon glyphicon-exclamation-sign"
aria-hidden=
"true"
></span>
The operator
<code>
is
</code>
is not supported to evaluate a parameter, the operator
<code>
==
</code>
must be prefered.
</div>
<div
id=
"parameters"
class=
"subgroup"
>
<h2>
Parameters
</h2>
...
...
docs/jflow-format.html
View file @
15c74f57
...
...
@@ -116,9 +116,11 @@
if nb_seq == 10: break
except:
raise jflow.InvalidFormatError("The provided file '" + ifile + "' is not a fasta file!")
</code></pre>
<span
class=
"glyphicon glyphicon-exclamation-sign"
aria-hidden=
"true"
></span>
Jflow provides
<code>
jflow.seqio
</code>
and
<code>
jflow.featureio
</code>
libraries where several file formats handler are available.
<div
class=
"alert alert-info"
role=
"alert"
>
<span
class=
"glyphicon glyphicon-exclamation-sign"
aria-hidden=
"true"
></span>
Jflow provides
<code>
jflow.seqio
</code>
and
<code>
jflow.featureio
</code>
libraries where several file formats handler are available.
</div>
</section>
<section
id=
"howuse"
class=
"group"
>
...
...
src/css/jflow.css
View file @
15c74f57
...
...
@@ -20,7 +20,9 @@
***************************************************************/
.handsontable
{
overflow
:
auto
;
overflow-x
:
auto
;
overflow-y
:
hidden
;
width
:
695px
;
}
.handsontable
td
.htInvalid
{
background-image
:
linear-gradient
(
to
bottom
,
#d9534f
0px
,
#c12e2a
100%
)
!important
;
...
...
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