Adding crs_converter to Galaxy ecology #119
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Really nice tool and quite an impressive xml !!;)
I tried to review what I could (I may double check later on)
I think the cheetah par may need some reviewing but I am afraid to make mistakes there ;)
PS : for the white spaces I did not correct all of them
Great work @Rassine !!
tools/crs_converter/CRS_macros.xml
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| <xml name='Y_options'> | ||
| <param name ='y_0' type='integer' value='0' | ||
| label='Y' help='False northing, northing at false origin or northing at projection centre |
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I don't know much about projection and I don't understand this help part. Maybe it could be clearer for non expert
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I agree with you, however these descriptions are directly from the PROJ.org website, I'm not certain I can provide a bether description, I will try but I'm not expert myself!
tools/crs_converter/CRS_macros.xml
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| <xml name='X_options'> | ||
| <param name ='x_0' type='integer' value='0' | ||
| label='X' help='False easting, easting at false origin or easting at projection centre |
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Same here for the help I don't understand much
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| <xml name='longitude_options'> | ||
| <param name ='lon_0' type='integer' value='0' | ||
| label='Longitude' help='Central meridian/longitude of natural origin, |
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Same the help is not clear for me
| <xml name='ellps_options'> | ||
| <param name ='ellps' type='select' checked='true' | ||
| label='Ellipsoid and Datum' help='The name of built-in ellipsoid definition. | ||
| See https://proj.org/en/9.4/usage/ellipsoids.html#ellipsoids for more informations.'> |
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more information in the help section ?
Co-authored-by: Marie Jossé <[email protected]>
Co-authored-by: Marie Jossé <[email protected]>
Co-authored-by: Marie Jossé <[email protected]>
Co-authored-by: Marie Jossé <[email protected]>
Co-authored-by: Marie Jossé <[email protected]>
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@Marie59 Thanks again for your review, I tried to put more information on the help parts you mentionend, but I belive with mixed succes, these description are very context dependent, looking directly at the projection on the PROJ website seems to be the easyest way to undersand the descriptions, I added direct links for each featured projection. |
Co-authored-by: Marie Jossé <[email protected]>
| https://proj.org/en/9.4/usage/projections.html | ||
| https://proj.org/en/9.4/geodesic.html | ||
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| https://proj.org/en/9.4/operations/projections/index.html |
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And same here put as I did before this way the user just have to click on the sentence and it open the page directly :)
tools/crs_converter/CRSconverter.xml
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| '$__tool_directory__/CRSconverter.R' | ||
| $os.path.join($input_file.extra_files_path, 'shapefile.shp') | ||
| '$output_file_format' | ||
| #for $param_name in $input_param.keys() ## this loop successively calls all the names and values of the PROJ string for each option of the conditional, it avoids a 100 lines command. |
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Can you maybe add a comment here how the commandline in the end should look like?
I guess something like + lat_ts + south ...?
| #if $param_name=='south' and $input_param[$param_name]=='false' | ||
| #pass | ||
| #elif $param_name=='south' and $input_param[$param_name]=='true' | ||
| ' ' '+' $param_name |
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| ' ' '+' $param_name | |
| ' + ' $param_name |
Would that also work?
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it would be : ' +' $param_name parameters and '+' are seperatated with others elements but not between themselves, blank spaces and '+' are separated because the R script needs to ignore the 1st blank space given as argument to create a proper PROJ string. this would work:
#if $param_name!='__current_case__'
#if $param_name=='south' and $input_param[$param_name]=='false'
#pass
#elif $param_name=='south' and $input_param[$param_name]=='true'
' +' $param_name
#elif $param_name=='approx' and $input_param[$param_name]=='false'
#pass
#elif $param_name=='approx' and $input_param[$param_name]=='true'
' +' $param_name
#elif $param_name=='lat_ts' and $input_param[$param_name]=='0'
#pass
#else
' ' '+' $param_name '='
$input_param[$param_name]
#end if
Co-authored-by: Marie Jossé <[email protected]>
Co-authored-by: Marie Jossé <[email protected]>
Co-authored-by: Marie Jossé <[email protected]>
Co-authored-by: Björn Grüning <[email protected]>
Co-authored-by: Marie Jossé <[email protected]>
CRS Converter transform coordinate reference systems of shapefiles using the st_transform function, the tool support a limited selection of interesting CRS, adding a new CRS can be done by simply adding a new condition inside the xml file and re-using or creating parrameters inside the marco file. The Cheetah script generates the PROJ string and handles special cases, this way I avoided having hundreds of lines of codes for each conditional statement and adding a new CRS does not require any modification of the cheetah command most of the time.
The output of the tool can eather be a shapefile, a pdf or an image.