Mercurial > repos > iuc > iedb_api
diff iedb_api.xml @ 0:fe3c43451319 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
| author | iuc |
|---|---|
| date | Fri, 28 Feb 2020 18:09:34 -0500 |
| parents | |
| children | a09849898387 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/iedb_api.xml Fri Feb 28 18:09:34 2020 -0500 @@ -0,0 +1,477 @@ +<tool id="iedb_api" name="IEDB" version="2.15.0"> + <description>MHC Binding prediction</description> + <macros> + <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples=""> + <conditional name="alleles"> + <param name="allelesrc" type="select" label="Alleles"> + <option value="history">From history</option> + <option value="entry">Entered</option> + </param> + <when value="history"> + <param name="allele_file" type="data" format="txt" label="Alleles file"> + <help>The dataset should have on allele per line. The allele may be followed by an optional comma-separated list of peptide lengths, e.g.: @HLALEN_EXAMPLES@</help> + </param> + </when> + <when value="entry"> + <param name="allele_text" type="text" size="80" label="Alleles"> + <help>Enter alleles separated by white space: @HLA_EXAMPLES@ (The peptide lengths may follow each allele: @HLALEN_EXAMPLES@)</help> + <validator type="regex" message="Doesn't appear to be a valid allele">^@HLA_REGEX@(\s+@HLA_REGEX@)*$</validator> + </param> + </when> + </conditional> + </xml> + </macros> + <requirements> + <requirement type="package" version="3.7">python</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ + #import re + python '${__tool_directory__}/iedb_api.py' + --prediction=$prediction.tool + --method=$prediction.method + #if $prediction.tool == 'bcell': + #if $prediction.window_size: + -w $prediction.window_size + #end if + #else + #if $prediction.tool == 'processing' and $prediction.proteasome: + --proteasome $prediction.proteasome + #end if + #if $prediction.alleles.allelesrc == 'history': + -A '$prediction.alleles.allele_file' + #else: + -A '$entered_alleles' + #end if + #end if + + #if $sequence.seqsrc == 'fasta': + -i '$sequence.seq_fasta' + #else if $sequence.seqsrc == 'tabular': + -i '$sequence.seq_tsv' + -c #echo int(str($sequence.pep_col)) - 1 + #if $sequence.id_col: + -C #echo int(str($sequence.id_col)) - 1 + #end if + #else: + -i '$entered_seqs' -c 1 -C 0 + #end if + -o '$output' + ]]></command> + <configfiles> + <configfile name="entered_alleles"><![CDATA[#slurp +#if $prediction.tool != 'bcell' and $prediction.alleles.allelesrc == 'entry' +#for $word in str($prediction.alleles.allele_text).strip().split(): +#if $word.find(',') > 0 +$word +#else +#set $allele = $word + ',' + str($prediction.lengths) +$allele +#end if +#end for +#end if +]]></configfile> + <configfile name="entered_seqs"><![CDATA[#slurp +#if $sequence.seqsrc == 'entry' +#for $i, $seq in enumerate(str($sequence.seq_text).strip().split()) +#set $seqid = $i + 1 +#set $seqtext = '\t'.join([str($seqid),$seq.strip()]) +$seqtext +#end for +#end if +]]></configfile> + </configfiles> + <inputs> + <conditional name="prediction"> + <param name="tool" type="select" label="Prediction"> + <option value="mhci">MHC-I Binding</option> + <option value="mhcii">MHC-II Binding</option> + <option value="processing">MHC-I Processing</option> + <option value="mhcnp">MHC-NP T-Cell Epitope</option> + <option value="bcell">Antibody Epitope Prediction</option> + </param> + <when value="mhci"> + <param name="method" type="select" label="prediction method"> + <option value="recommended" selected="true">recommended</option> + <option value="consensus">consensus</option> + <option value="netmhcpan">netmhcpan</option> + <option value="ann">ann</option> + <option value="smmpmbec">smmpmbec</option> + <option value="smm">smm</option> + <option value="comblib_sidney2008">comblib_sidney2008</option> + <option value="netmhccons">netmhccons</option> + <option value="pickpocket">pickpocket</option> + </param> + <expand macro="alleles" hla_regex="(HLA-[A-CEG]\*[0-8][[0-9]:[0-9][0-9][0-9]*|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-5]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/> + <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> + <help>Used for any alleles which don't include specified lengths</help> + <option value="8" selected="true">8</option> + <option value="9">9</option> + <option value="10">10</option> + <option value="11">11</option> + <option value="12">12</option> + <option value="13">13</option> + <option value="14">14</option> + <option value="15">15</option> + </param> + + </when> + <when value="mhcii"> + <param name="method" type="select" label="prediction method"> + <option value="recommended" selected="true">recommended</option> + <option value="consensus3">consensus3</option> + <option value="NetMHCIIpan">NetMHCIIpan</option> + <option value="nn_align">nn_align</option> + <option value="smm_align">smm_align</option> + <option value="comblib">comblib</option> + <option value="tepitope">tepitope</option> + </param> + <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"/> + <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> + <help>Used for any alleles which don't include specified lengths</help> + <option value="asis">asis</option> + <option value="11">11</option> + <option value="12">12</option> + <option value="13">13</option> + <option value="14">14</option> + <option value="15" selected="true">15</option> + <option value="16">16</option> + <option value="17">17</option> + <option value="18">18</option> + <option value="19">19</option> + <option value="20">20</option> + <option value="21">21</option> + <option value="22">22</option> + <option value="23">23</option> + <option value="24">24</option> + <option value="25">25</option> + <option value="26">26</option> + <option value="27">27</option> + <option value="28">28</option> + <option value="29">29</option> + <option value="30">30</option> + </param> + </when> + <when value="processing"> + <param name="method" type="select" label="prediction method"> + <option value="recommended" selected="true">recommended</option> + <option value="consensus">consensus</option> + <option value="netmhcpan">netmhcpan</option> + <option value="ann">ann</option> + <option value="smmpmbec">smmpmbec</option> + <option value="smm">smm</option> + <option value="comblib_sidney2008">comblib_sidney2008</option> + </param> + <param name="proteasome" type="select" label="proteasome type"> + <option value="immuno">immuno</option> + <option value="constitutive">constitutive</option> + </param> + <expand macro="alleles" hla_regex="(HLA-[A-CE]\*[0-8][[0-9]:[0-9][0-9]|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-4]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/> + <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> + <help>Used for any alleles which don't include specified lengths</help> + <option value="8" selected="true">8</option> + <option value="9">9</option> + <option value="10">10</option> + <option value="11">11</option> + <option value="12">12</option> + <option value="13">13</option> + <option value="14">14</option> + </param> + </when> + <when value="mhcnp"> + <param name="method" type="select" label="prediction method"> + <option value="mhcnp" selected="true">mhcnp</option> + <option value="netmhcpan">netmhcpan</option> + </param> + <expand macro="alleles" hla_regex="(HLA-(A\*02:01|B\*07:02|B\*35:01|B\*44:03|B\*53:01|B\*57:01)|H-2-[DK]b)(,[8-9]|1[0-1])*" hla_examples="HLA-A*02:01 H-2-Db" hlalen_examples="HLA-A*02:01,8,9,10"/> + <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> + <help>Used for any alleles which don't include specified lengths</help> + <option value="8" selected="true">8</option> + <option value="9">9</option> + <option value="10">10</option> + <option value="11">11</option> + </param> + </when> + <when value="bcell"> + <param name="method" type="select" label="prediction method"> + <option value="Bepipred" selected="true">Bepipred</option> + <option value="Chou-Fasman">Chou-Fasman</option> + <option value="Emini">Emini</option> + <option value="Karplus-Schulz">Karplus-Schulz</option> + <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option> + <option value="Parker">Parker</option> + </param> + <param name="window_size" type="integer" value="" optional="true" min="1" label="window_size" help="window_size should be less than the sequence length, and less than 8 for Karplus-Schulz method"/> + </when> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" type="select" label="Peptide sequences"> + <option value="fasta">Fasta file</option> + <option value="tabular">From tabular</option> + <option value="entry"></option> + </param> + <when value="fasta"> + <param name="seq_fasta" type="data" format="fasta" label="Peptide Sequence Fasta"/> + </when> + <when value="tabular"> + <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/> + <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" /> + <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/> + </when> + <when value="entry"> + <param name="seq_text" type="text" label="Peptide Sequence"/> + </when> + </conditional> + + </inputs> + <outputs> + <!-- + <data name="output" format="tabular"/> + --> + <data name="output" format="tabular" label="IEDB ${prediction.tool} ${prediction.method}"/> + <data name="output2" format="tabular" label="IEDB ${prediction.tool} ${prediction.method} residue scores" from_work_dir="iedb_results2"> + <filter>prediction['method'].startswith('Bepipred')</filter> + </data> + </outputs> + <tests> + <!-- test1 --> + <test> + <conditional name="prediction"> + <param name="tool" value="mhci"/> + <param name="method" value="recommended"/> + <conditional name="alleles"> + <param name="allelesrc" value="entry"/> + <param name="allele_text" value="HLA-A*01:01,9"/> + </conditional> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="entry"/> + <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="LYNTVATLY" /> + </assert_contents> + </output> + </test> + <!-- test2 --> + <test> + <conditional name="prediction"> + <param name="tool" value="mhci"/> + <param name="method" value="recommended"/> + <conditional name="alleles"> + <param name="allelesrc" value="history"/> + <param name="allele_file" ftype="tabular" value="alleles.tsv"/> + </conditional> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="fasta"/> + <param name="seq_fasta" ftype="fasta" value="seqs.fa"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="peptide1" /> + <has_text text="HKVPRRLLK" /> + </assert_contents> + </output> + </test> + <!-- test3 --> + <test> + <conditional name="prediction"> + <param name="tool" value="mhci"/> + <param name="method" value="recommended"/> + <conditional name="alleles"> + <param name="allelesrc" value="history"/> + <param name="allele_file" ftype="tabular" value="alleles.tsv"/> + </conditional> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="tabular"/> + <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/> + <param name="pep_col" value="3"/> + <param name="id_col" value="1"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="peptide1" /> + <has_text text="HKVPRRLLK" /> + </assert_contents> + </output> + </test> + <!-- test4 --> + <test> + <conditional name="prediction"> + <param name="tool" value="mhcii"/> + <param name="method" value="recommended"/> + <conditional name="alleles"> + <param name="allelesrc" value="entry"/> + <param name="allele_text" value="DPA1*01/DPB1*04:01"/> + </conditional> + <param name="lengths" value="asis"/> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="entry"/> + <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="LYNTVATLY" /> + </assert_contents> + </output> + </test> + <!-- test5 --> + <test> + <conditional name="prediction"> + <param name="tool" value="processing"/> + <param name="method" value="recommended"/> + <conditional name="alleles"> + <param name="allelesrc" value="entry"/> + <param name="allele_text" value="HLA-A*01:01,8 HLA-A*02:01,9"/> + </conditional> + <param name="proteasome" value="constitutive"/> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="entry"/> + <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="LYNTVATLY" /> + </assert_contents> + </output> + </test> + <!-- test6 --> + <test> + <conditional name="prediction"> + <param name="tool" value="mhcnp"/> + <param name="method" value="mhcnp"/> + <conditional name="alleles"> + <param name="allelesrc" value="entry"/> + <param name="allele_text" value="HLA-A*02:01,9"/> + </conditional> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="entry"/> + <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="LYNTVATLY" /> + </assert_contents> + </output> + </test> + <!-- test7 --> + <test> + <conditional name="prediction"> + <param name="tool" value="bcell"/> + <param name="method" value="Emini"/> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="entry"/> + <param name="seq_text" value="VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTE"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="VLSEGE" /> + </assert_contents> + </output> + </test> + <!-- test8 --> + <test> + <conditional name="prediction"> + <param name="tool" value="bcell"/> + <param name="method" value="Bepipred"/> + <param name="window_size" value="9"/> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="fasta"/> + <param name="seq_fasta" ftype="fasta" value="bcell.fa"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="ADVAGH" /> + </assert_contents> + </output> + </test> + + </tests> + <help><![CDATA[ +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. + +This tool retrieves epitope binding information about input peptide sequences by using the RESTful web services provided by IEDB. +The webservices are described at: http://tools.immuneepitope.org/main/tools-api/ +That page also describes how to retrieve the available HLA alleles for class of epitope binding. + +**INPUTS** + + peptide sequences from a fasta file or a column in a tabular file + + HLA alleles either entered as text or one per line in a text file + + +**OUTPUTS** + + A tabular file containing the results returned from the IEDB web service + +**Typical Workflow for Human MHC I Binding Prediction** + +The RNAseq data for the subject would be used for: + + - HLA prediction by seq2HLA + - Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta + + +.. image:: $PATH_TO_IMAGES/IEDB_Workflow_QueryTabular.png + :width: 584 + :height: 430 + +.. note:: The seq2HLA ClassI.HLAgenotype4digits output needs to be converted for IEDB alleles. + +The seq2HLA ClassI.HLAgenotype4digits output: + +.. image:: $PATH_TO_IMAGES/seq2HLA_ClassI.HLAgenotype4digits.png + :width: 285 + :height: 77 + +Needs to be converted into IEDB formatted alleles: + +.. image:: $PATH_TO_IMAGES/IEDB_formatted_alleles.png + :width: 74 + :height: 81 + +In the workflow above QueryTabular tool converts the alleles: + + - Filter Dataset Input + + * skip leading lines - *skip lines:* 1 + * select columns - *columns:* 2,4 + * regex replace value in column - *column:* 1 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1 + * regex replace value in column - *column:* 2 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1 + + - SQL Query to generate tabular output + + * SELECT c1 FROM t1 UNION SELECT c2 FROM t1 + + +The IEDB formatting can also be performed by TextProcessing tools: + +.. image:: $PATH_TO_IMAGES/TextProcessingConversion.png + :width: 608 + :height: 87 + +The TextProcessing steps to convert the alleles: + + - Remove beginning - removes the header line + - Replace Text - picks Allele 1 and Allele 2 from each line and reformats each on a separate line + + * *Find pattern:* ^.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*$ + * *Replace with:* HLA-\\1\\nHLA-\\2 + + - Unique - remove duplicates + + + ]]></help> + <citations> + <citation type="doi">10.1093/nar/gku938</citation> + </citations> +</tool>