Mercurial > repos > jjohnson > iedb_api

comparison iedb_api.xml @ 3:153d5fa7af53 draft

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"
author jjohnson
date Wed, 26 Feb 2020 16:27:06 -0500
parents 883cdf0ffae5
children a14128950578
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2:883cdf0ffae5 3:153d5fa7af53
83 #else: 83 #else:
84 #for $seq in str($sequence.seq_text).strip().split(): 84 #for $seq in str($sequence.seq_text).strip().split():
85 -s $seq.strip() 85 -s $seq.strip()
86 #end for 86 #end for
87 #end if 87 #end if
88 -o $output 88 -o '$output'
89 ]]></command> 89 ]]></command>
90 <inputs> 90 <inputs>
91 <conditional name="prediction"> 91 <conditional name="prediction">
92 <param name="tool" type="select" label="Prediction"> 92 <param name="tool" type="select" label="Prediction">
93 <option value="mhci">MHC-I Binding</option> 93 <option value="mhci">MHC-I Binding</option>
130 <option value="nn_align">nn_align</option> 130 <option value="nn_align">nn_align</option>
131 <option value="smm_align">smm_align</option> 131 <option value="smm_align">smm_align</option>
132 <option value="comblib">comblib</option> 132 <option value="comblib">comblib</option>
133 <option value="tepitope">tepitope</option> 133 <option value="tepitope">tepitope</option>
134 </param> 134 </param>
135 <expand macro="alleles" hla_regex="((DPA1\*0[1-3](:0[1-3])?/DPB1\*0[1-6]:0[12]|DQA1\*0[1-5]:0[12]/DQB1\*0[2-6]:0[12]|DRB[1-5]\*[01][1-9]:0[1-5]|H2-IA[bd]),(asis|[1-2][0-9]|30))*" hla_examples="DPA1*01/DPB1*04:01 HLA-DRB1*01:01 H2-IAb" hlalen_examples="DPA1*01/DPB1*04:01,11,15"/> 135 <expand macro="alleles" hla_regex="(DPA1\*0[1-3](:0[1-3])?/DPB1\*0[1-6]:0[12]|DQA1\*0[1-5]:0[12]/DQB1\*0[2-6]:0[12]|DRB[1-5]\*[01][1-9]:0[1-5]|H2-IA[bd])(,(asis|[1-2][0-9]|30))*" hla_examples="DPA1*01/DPB1*04:01 HLA-DRB1*01:01 H2-IAb" hlalen_examples="DPA1*01/DPB1*04:01,11,15"/>
136 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> 136 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
137 <help>Used for any alleles which don't include specified lengths</help> 137 <help>Used for any alleles which don't include specified lengths</help>
138 <option value="asis">asis</option> 138 <option value="asis">asis</option>
139 <option value="11">11</option> 139 <option value="11">11</option>
140 <option value="12">12</option> 140 <option value="12">12</option>
223 <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/> 223 <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/>
224 <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" /> 224 <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" />
225 <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/> 225 <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/>
226 </when> 226 </when>
227 <when value="entry"> 227 <when value="entry">
228 <param name="seq_text" type="text" size="80" label="Peptide Sequence"/> 228 <param name="seq_text" type="text" label="Peptide Sequence"/>
229 </when> 229 </when>
230 </conditional> 230 </conditional>
231 231
232 </inputs> 232 </inputs>
233 <outputs> 233 <outputs>
403 403
404 **Typical Workflow for Human MHC I Binding Prediction** 404 **Typical Workflow for Human MHC I Binding Prediction**
405 405
406 The RNAseq data for the subject would be used for: 406 The RNAseq data for the subject would be used for:
407 407
408 - HLA prediction by seq2HLA_ 408 - HLA prediction by seq2HLA
409 - Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta 409 - Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta
410 410
411 .. _seq2HLA: https://toolshed.g2.bx.psu.edu/view/iuc/seq2hla/52bba1cd3823
412 411
413 .. image:: $PATH_TO_IMAGES/IEDB_Workflow_QueryTabular.png 412 .. image:: $PATH_TO_IMAGES/IEDB_Workflow_QueryTabular.png
414 :width: 584 413 :width: 584
415 :height: 430 414 :height: 430
416 415
426 425
427 .. image:: $PATH_TO_IMAGES/IEDB_formatted_alleles.png 426 .. image:: $PATH_TO_IMAGES/IEDB_formatted_alleles.png
428 :width: 74 427 :width: 74
429 :height: 81 428 :height: 81
430 429
431 In the workflow above QueryTabular_ tool converts the alleles: 430 In the workflow above QueryTabular tool converts the alleles:
432 431
433 - Filter Dataset Input 432 - Filter Dataset Input
434 433
435 * skip leading lines - *skip lines:* 1 434 * skip leading lines - *skip lines:* 1
436 * select columns - *columns:* 2,4 435 * select columns - *columns:* 2,4
439 438
440 - SQL Query to generate tabular output 439 - SQL Query to generate tabular output
441 440
442 * SELECT c1 FROM t1 UNION SELECT c2 FROM t1 441 * SELECT c1 FROM t1 UNION SELECT c2 FROM t1
443 442
444 .. _QueryTabular: https://toolshed.g2.bx.psu.edu/view/iuc/query_tabular/0c95a3f1654f 443
445 444 The IEDB formatting can also be performed by TextProcessing tools:
446
447 The IEDB formatting can also be performed by TextProcessing_ tools:
448
449 .. _TextProcessing: https://toolshed.g2.bx.psu.edu/view/bgruening/text_processing/0a8c6b61f0f4
450 445
451 .. image:: $PATH_TO_IMAGES/TextProcessingConversion.png 446 .. image:: $PATH_TO_IMAGES/TextProcessingConversion.png
452 :width: 608 447 :width: 608
453 :height: 87 448 :height: 87
454 449