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comparison PDAUG_Peptide_CD_Spectral_Analysis/PDAUG_Peptide_CD_Spectral_Analysis.xml @ 6:370b68568ba2 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author jay
date Sun, 31 Jan 2021 02:46:28 +0000
parents 9bbad349f44c
children
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5:95900530d661 6:370b68568ba2
68 68
69 <conditional name='SelMethods' > 69 <conditional name='SelMethods' >
70 70
71 <param name="Methods" type="select" label="Circular dichroism data analysis options" help="Circular dichroism data analysis options" > 71 <param name="Methods" type="select" label="Circular dichroism data analysis options" help="Circular dichroism data analysis options" >
72 <option value="calc_ellipticity">Calculate Ellipticity</option> 72 <option value="calc_ellipticity">Calculate Ellipticity</option>
73 <option value="PlotData">Plot Data</option> 73 <option value="PlotData">Generate CD Plots</option>
74 <option value="Dichroweb">Save data in DichroWeb readable format</option> 74 <option value="Dichroweb">Save Data in DichroWeb Readable Format</option>
75 <option value="helicity">Calculate the percentage of helicity</option> 75 <option value="helicity">Calculate the Percentage of Helicity</option>
76 </param> 76 </param>
77 77
78 <when value="calc_ellipticity"> 78 <when value="calc_ellipticity">
79 <param name="ellipticity" type="select" label="Ellipticity type" argument="-T" help="Methods to calculate the molar ellipticity for all loaded data"> 79 <param name="ellipticity" type="select" label="Ellipticity type" argument="-T" help="Methods to calculate the molar ellipticity for all loaded data">
80 <option value="calc_molar_ellipticity">Calculate Molar Ellipticity</option> 80 <option value="calc_molar_ellipticity">Calculate Molar Ellipticity</option>
301 **What it does** 301 **What it does**
302 302
303 This tool handles circular dichroism data files and calculates several ellipticity and helicity values. The class can handle data files of the Applied Photophysics type. For explanations of different units used in CD spectroscopy, visit https://www.photophysics.com/resources/7-cd-units-conversions. Provided with four different options. 303 This tool handles circular dichroism data files and calculates several ellipticity and helicity values. The class can handle data files of the Applied Photophysics type. For explanations of different units used in CD spectroscopy, visit https://www.photophysics.com/resources/7-cd-units-conversions. Provided with four different options.
304 304
305 * **Calculate Ellipticity** Calculates molar and mean residue ellipticity. 305 * **Calculate Ellipticity** Calculates molar and mean residue ellipticity.
306 * **Plot Data** Generates circular_dichroism plots for all read data in the initial directory. 306 * **Generate CD Plots** Generates circular_dichroism plots for all read data in the initial directory.
307 * **Save data in DichroWeb readable format** Method to save the calculated CD data into DichroWeb readable format (semi-colon separated). The produced files can then directly be uploaded to the DichroWeb analysis tool. 307 * **Save Data in DichroWeb Readable Format** Method to save the calculated CD data into DichroWeb readable format (semi-colon separated). The produced files can then directly be uploaded to the DichroWeb analysis tool.
308 * **Calculate the percentage of helicity** Method to calculate the percentage of helicity out of the mean residue ellipticity data. The calculation is based on the formula by Fairlie and co-workers. 308 * **Calculate the Percentage of Helicity<** Method to calculate the percentage of helicity out of the mean residue ellipticity data. The calculation is based on the formula by Fairlie and co-workers.
309 309
310 ----- 310 -----
311 311
312 **Inputs** 312 **Inputs**
313 313
314 **1** calc_ellipticity 314 **1** Calculate Ellipticity
315 * **--Type** 315 * **--Type**
316 * **--Wmin** smallest wavelength measured 316 * **--Wmin** smallest wavelength measured
317 * **--Wmax** highest wavelength measured 317 * **--Wmax** highest wavelength measured
318 * **--Amide** specifies whether the sequences have amidated C-termini 318 * **--Amide** specifies whether the sequences have amidated C-termini
319 * **--Pathlen** cuvette path length in mm 319 * **--Pathlen** cuvette path length in mm
320 320
321 **2** PlotData 321 **2** Generate CD Plots
322 * **--Type** 322 * **--Type**
323 * **--Wmin** smallest wavelength measured 323 * **--Wmin** smallest wavelength measured
324 * **--Wmax** highest wavelength measured 324 * **--Wmax** highest wavelength measured
325 * **--Amide** specifies whether the sequences have amidated C-termini 325 * **--Amide** specifies whether the sequences have amidated C-termini
326 * **--Pathlen** cuvette path length in mm 326 * **--Pathlen** cuvette path length in mm
327 327
328 **3** Dicroweb 328 **3** Save Data in DichroWeb Readable Format
329 * **--Type** 329 * **--Type**
330 * **--Wmin** smallest wavelength measured 330 * **--Wmin** smallest wavelength measured
331 * **--Wmax** highest wavelength measured 331 * **--Wmax** highest wavelength measured
332 * **--Amide** specifies whether the sequences have amidated C-termini 332 * **--Amide** specifies whether the sequences have amidated C-termini
333 * **--Pathlen** cuvette path length in mm 333 * **--Pathlen** cuvette path length in mm
334 334
335 **4** helicity 335 **4** Calculate the Percentage of Helicity
336 * **--Type** 336 * **--Type**
337 * **--Wmin** smallest wavelength measured 337 * **--Wmin** smallest wavelength measured
338 * **--Wmax** highest wavelength measured 338 * **--Wmax** highest wavelength measured
339 * **--Amide** specifies whether the sequences have amidated C-termini 339 * **--Amide** specifies whether the sequences have amidated C-termini
340 * **--Pathlen** cuvette path length in mm 340 * **--Pathlen** cuvette path length in mm
341 * **--temperature** experiment temperature in °C 341 * **--temperature** experiment temperature in °C
342 * **--k** {float, 2.4 - 4.5} finite length correction factor. Can be adapted to the helicity of a known peptide. 342 * **--k** {float, 2.4 - 4.5} finite length correction factor. Can be adapted to the helicity of a known peptide.
343 * **--Induction** whether the helical induction upon changing from one solvent to another should be calculated. 343 * **--Induction** whether the helical induction upon changing from one solvent to another should be calculated.
344
345 344
346 ----- 345 -----
347 346
348 **Outputs** 347 **Outputs**
349 * **Calculate Ellipticity** Return molar or mean residue ellipticity as a tabular file. 348 * **Calculate Ellipticity** Return molar or mean residue ellipticity as a tabular file.