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comparison iedb_api.xml @ 4:a14128950578 draft default tip

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
author jjohnson
date Fri, 28 Feb 2020 15:45:14 -0500
parents 153d5fa7af53
children
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3:153d5fa7af53 4:a14128950578
22 </xml> 22 </xml>
23 </macros> 23 </macros>
24 <requirements> 24 <requirements>
25 <requirement type="package" version="3.7">python</requirement> 25 <requirement type="package" version="3.7">python</requirement>
26 </requirements> 26 </requirements>
27
27 <command detect_errors="exit_code"><![CDATA[ 28 <command detect_errors="exit_code"><![CDATA[
28 #import re 29 #import re
29 python '${__tool_directory__}/iedb_api.py' 30 python '${__tool_directory__}/iedb_api.py'
30 --prediction=$prediction.tool 31 --prediction=$prediction.tool
31 --method=$prediction.method 32 --method=$prediction.method
36 #else 37 #else
37 #if $prediction.tool == 'processing' and $prediction.proteasome: 38 #if $prediction.tool == 'processing' and $prediction.proteasome:
38 --proteasome $prediction.proteasome 39 --proteasome $prediction.proteasome
39 #end if 40 #end if
40 #if $prediction.alleles.allelesrc == 'history': 41 #if $prediction.alleles.allelesrc == 'history':
41 #for $line in open(str($prediction.alleles.allele_file)): 42 -A '$prediction.alleles.allele_file'
42 #set $fields = $line.strip().split(',')
43 #set $allele = $fields[0].strip()
44 #if len($allele) > 0:
45 #if len($fields) > 1:
46 #for $alen in $fields[1:]:
47 -a '$allele' -l $alen
48 #end for
49 #else:
50 #for $alen in str($prediction.lengths).split(','):
51 -a '$allele' -l $alen
52 #end for
53 #end if
54 #end if
55 #end for
56 #else: 43 #else:
57 #for $word in str($prediction.alleles.allele_text).strip().split(): 44 -A '$entered_alleles'
58 #set $fields = $word.strip().split(',')
59 #set $allele = $fields[0].strip()
60 #if len($allele) > 0:
61 #if len($fields) > 1:
62 #for $alen in $fields[1:]:
63 -a '$allele' -l $alen
64 #end for
65 #else:
66 #for $alen in str($prediction.lengths).split(','):
67 -a '$allele' -l $alen
68 #end for
69 #end if
70 #end if
71 #end for
72 #end if 45 #end if
73 #end if 46 #end if
74 47
75 #if $sequence.seqsrc == 'fasta': 48 #if $sequence.seqsrc == 'fasta':
76 -i '$sequence.seq_fasta' 49 -i '$sequence.seq_fasta'
79 -c #echo int(str($sequence.pep_col)) - 1 52 -c #echo int(str($sequence.pep_col)) - 1
80 #if $sequence.id_col: 53 #if $sequence.id_col:
81 -C #echo int(str($sequence.id_col)) - 1 54 -C #echo int(str($sequence.id_col)) - 1
82 #end if 55 #end if
83 #else: 56 #else:
84 #for $seq in str($sequence.seq_text).strip().split(): 57 -i '$entered_seqs' -c 1 -C 0
85 -s $seq.strip()
86 #end for
87 #end if 58 #end if
88 -o '$output' 59 -o '$output'
89 ]]></command> 60 ]]></command>
61 <configfiles>
62 <configfile name="entered_alleles"><![CDATA[#slurp
63 #if $prediction.tool != 'bcell' and $prediction.alleles.allelesrc == 'entry'
64 #for $word in str($prediction.alleles.allele_text).strip().split():
65 #if $word.find(',') > 0
66 $word
67 #else
68 #set $allele = $word + ',' + str($prediction.lengths)
69 $allele
70 #end if
71 #end for
72 #end if
73 ]]></configfile>
74 <configfile name="entered_seqs"><![CDATA[#slurp
75 #if $sequence.seqsrc == 'entry'
76 #for $i, $seq in enumerate(str($sequence.seq_text).strip().split())
77 #set $seqid = $i + 1
78 #set $seqtext = '\t'.join([str($seqid),$seq.strip()])
79 $seqtext
80 #end for
81 #end if
82 ]]></configfile>
83 </configfiles>
90 <inputs> 84 <inputs>
91 <conditional name="prediction"> 85 <conditional name="prediction">
92 <param name="tool" type="select" label="Prediction"> 86 <param name="tool" type="select" label="Prediction">
93 <option value="mhci">MHC-I Binding</option> 87 <option value="mhci">MHC-I Binding</option>
94 <option value="mhcii">MHC-II Binding</option> 88 <option value="mhcii">MHC-II Binding</option>
130 <option value="nn_align">nn_align</option> 124 <option value="nn_align">nn_align</option>
131 <option value="smm_align">smm_align</option> 125 <option value="smm_align">smm_align</option>
132 <option value="comblib">comblib</option> 126 <option value="comblib">comblib</option>
133 <option value="tepitope">tepitope</option> 127 <option value="tepitope">tepitope</option>
134 </param> 128 </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"/> 129 <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]|(HLA-)?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"> 130 <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> 131 <help>Used for any alleles which don't include specified lengths</help>
138 <option value="asis">asis</option> 132 <option value="asis">asis</option>
139 <option value="11">11</option> 133 <option value="11">11</option>
140 <option value="12">12</option> 134 <option value="12">12</option>
380 <assert_contents> 374 <assert_contents>
381 <has_text text="VLSEGE" /> 375 <has_text text="VLSEGE" />
382 </assert_contents> 376 </assert_contents>
383 </output> 377 </output>
384 </test> 378 </test>
379 <!-- test8 -->
380 <test>
381 <conditional name="prediction">
382 <param name="tool" value="bcell"/>
383 <param name="method" value="Bepipred"/>
384 <param name="window_size" value="9"/>
385 </conditional>
386 <conditional name="sequence">
387 <param name="seqsrc" value="fasta"/>
388 <param name="seq_fasta" ftype="fasta" value="bcell.fa"/>
389 </conditional>
390 <output name="output">
391 <assert_contents>
392 <has_text text="ADVAGH" />
393 </assert_contents>
394 </output>
395 </test>
396
385 </tests> 397 </tests>
386 <help><![CDATA[ 398 <help><![CDATA[
387 The IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases. It offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species. 399 The IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases. It offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species.
388 400
389 This tool retrieves epitope binding information about input peptide sequences by using the RESTful web services provided by IEDB. 401 This tool retrieves epitope binding information about input peptide sequences by using the RESTful web services provided by IEDB.