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comparison pathwaymatcher.xml @ 4:3e510701a712 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
author galaxyp
date Sun, 14 Jul 2019 05:09:33 -0400
parents 2cd67294abbd
children a2ab72e994dc
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3:2cd67294abbd 4:3e510701a712
2 <description> 2 <description>
3 PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome. 3 PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome.
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@PATHWAYMATCHER_VERSION@">1.9.1</token> 6 <token name="@PATHWAYMATCHER_VERSION@">1.9.1</token>
7 <token name="@TOOL_SUBVERSION@">1</token> 7 <token name="@TOOL_SUBVERSION@">2</token>
8 <xml name="input_fasta"> 8 <xml name="input_fasta">
9 <param format="fasta" name="input_database" type="data" label="Protein Database" 9 <param format="fasta" name="input_database" type="data" label="Protein Database"
10 help="Select FASTA database from history"/> 10 help="Select FASTA database from history"/>
11 </xml> 11 </xml>
12 </macros> 12 </macros>
16 </requirements> 16 </requirements>
17 <stdio> 17 <stdio>
18 <exit_code range="1:" level="fatal" description="Job Failed" /> 18 <exit_code range="1:" level="fatal" description="Job Failed" />
19 <regex match="java.*Exception" level="fatal" description="Java Exception"/> 19 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
20 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> 20 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
21 <regex match="filename not matched: reports/proteins_proteoforms.txt" level="fatal" description="PeptideShaker archive does not contain the proteoforms file. It may have been created by a 1.x PeptideShaker version."/>
21 </stdio> 22 </stdio>
22 <command> 23 <command>
23 <![CDATA[ 24 <![CDATA[
24 #from datetime import datetime 25 #from datetime import datetime
25 #import json 26 #import json
31 32
32 mkdir output; 33 mkdir output;
33 cwd=`pwd`; 34 cwd=`pwd`;
34 export HOME=\$cwd; 35 export HOME=\$cwd;
35 36
36 ## If we use peptideshaker files as inputs, firstly we need to uncompress their proteoforms files. 37 ## If we use peptideshaker 2.x files as inputs, firstly we need to uncompress their proteoforms files.
37 #for $i, $s in enumerate($match_types) 38 #for $i, $s in enumerate($match_types)
38 #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms" 39 #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms"
39 ##unzip -l $s.match_type.input_peptideshakerzip_proteoforms; 40 unzip -j '${$s.match_type.input_peptideshakerzip_proteoforms}' 'reports/proteins_proteoforms.txt' -d './';
40 unzip -j '${$s.match_type.input_peptideshakerzip_proteoforms}' 'output_reports/proteoforms.txt' -d './'; 41 mv proteins_proteoforms.txt ps_proteoforms_'${$i}'.txt;
41 mv proteoforms.txt ps_proteoforms_'${$i}'.txt;
42 #end if 42 #end if
43 #end for 43 #end for
44 44
45 ##################### 45 #####################
46 ## Pathway Matcher ## 46 ## Pathway Matcher ##
47 ##################### 47 #####################
48 (pathwaymatcher 48 (pathwaymatcher
49 49
50 #for $i, $s in enumerate($match_types) 50 #for $i, $s in enumerate($match_types)
51
52 51
53 ## PROTEOFORMS 52 ## PROTEOFORMS
54 53
55 #if $s.match_type.match_type_selector == "proteoforms" 54 #if $s.match_type.match_type_selector == "proteoforms"
56 #if $s.match_type.proteoform_match_criteria: 55 #if $s.match_type.proteoform_match_criteria:
145 144
146 ## We create a folder to contain graphs files. 145 ## We create a folder to contain graphs files.
147 #if $output_options.output_graphs: 146 #if $output_options.output_graphs:
148 mkdir "graphs"; 147 mkdir "graphs";
149 #end if 148 #end if
150
151 #if 'gg' in $output_graphs_list: 149 #if 'gg' in $output_graphs_list:
152 mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv" ; 150 mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv" ;
153 #end if 151 #end if
154
155 #if 'gu' in $output_graphs_list: 152 #if 'gu' in $output_graphs_list:
156 mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv"; 153 mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv";
157 #end if 154 #end if
158
159 #if 'gp' in $output_graphs_list: 155 #if 'gp' in $output_graphs_list:
160 mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv"; 156 mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv";
161 #end if 157 #end if
162 158
163 exit_code_for_galaxy=\$?; 159 exit_code_for_galaxy=\$?;
170 <repeat name="match_types" title="Match" min="1"> 166 <repeat name="match_types" title="Match" min="1">
171 <conditional name="match_type"> 167 <conditional name="match_type">
172 <param name="match_type_selector" type="select" label="Match type" 168 <param name="match_type_selector" type="select" label="Match type"
173 help=""> 169 help="">
174 <option value="proteoforms">Proteoforms</option> 170 <option value="proteoforms">Proteoforms</option>
175 <option value="peptideshakerzip_proteoforms">Proteoforms from Peptideshaker Archive</option> 171 <option value="peptideshakerzip_proteoforms">Proteoforms from Peptideshaker 2.x Archive</option>
176 <option value="gene">Genes</option> 172 <option value="gene">Genes</option>
177 <option value="uniprot">Proteins - UniProt Accession list</option> 173 <option value="uniprot">Proteins - UniProt Accession list</option>
178 <option value="ensembl">Proteins - Ensembl identifier list</option> 174 <option value="ensembl">Proteins - Ensembl identifier list</option>
179 <option value="vcf">Genetic variants - Variant Call Format Specification</option> 175 <option value="vcf">Genetic variants - Variant Call Format Specification</option>
180 <option value="chrbp">Genetic variants - Chromosomes and base pairs</option> 176 <option value="chrbp">Genetic variants - Chromosomes and base pairs</option>
181 <option value="rsid">Genetic variants - SNP rsId list</option> 177 <option value="rsid">Genetic variants - SNP rsId list</option>
182 <option value="peptide">Peptides - Simple list</option> 178 <option value="peptide">Peptides - Simple list</option>
183 <option value="modifiedpeptide">Peptides - Peptide List with PTM types and sites</option> 179 <option value="modifiedpeptide">Peptides - Peptide List with PTM types and sites</option>
184
185 </param> 180 </param>
186 181
187 182
188 <!-- Proteoforms --> 183 <!-- Proteoforms -->
189 <when value="proteoforms"> 184 <when value="proteoforms">
200 <option value="SUPERSET_NO_TYPES">SUPERSET NO TYPES</option> 195 <option value="SUPERSET_NO_TYPES">SUPERSET NO TYPES</option>
201 <option value="SUBSET" selected="True">SUBSET</option> 196 <option value="SUBSET" selected="True">SUBSET</option>
202 <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option> 197 <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option>
203 <option value="ONE">ONE</option> 198 <option value="ONE">ONE</option>
204 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option> 199 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>
200 <option value="ACCESSION">ACCESSION</option>
205 </param> 201 </param>
206 202
207 <param name="proteoform_range" type="integer" value="0" label="Integer range of error for PTM sites" optional="true" 203 <param name="proteoform_range" type="integer" value="0" label="Integer range of error for PTM sites" optional="true"
208 help="Plus minus positions for the same PTM site"/> 204 help="Plus minus positions for the same PTM site"/>
209 </when> 205 </when>
210 206
211 <when value="peptideshakerzip_proteoforms"> 207 <when value="peptideshakerzip_proteoforms">
212 <param format="zip" name="input_peptideshakerzip_proteoforms" type="data" label="Proteoforms from Peptideshaker Archive" 208 <param format="zip" name="input_peptideshakerzip_proteoforms" type="data" label="Proteoforms from Peptideshaker 2.x Archive"
213 help="A proteoform defines a specific state of a protein. 209 help="A proteoform defines a specific state of a protein.
214 It is composed by the protein UniProt accession, isoform and set of post translational modifications. 210 It is composed by the protein UniProt accession, isoform and set of post translational modifications.
215 The input file contains one line for each proteoform. Each PTM is specified using a modification 211 The input file contains one line for each proteoform. Each PTM is specified using a modification
216 identifier and a site, separated by ':'(semicolon). For example: '00046:133'. 212 identifier and a site, separated by ':'(semicolon). For example: '00046:133'.
217 The identifier is a 5 digit id from the PSI-MOD Protein Modification Onthology [6]."/> 213 The identifier is a 5 digit id from the PSI-MOD Protein Modification Onthology [6]."/>
222 <option value="SUPERSET_NO_TYPES">SUPERSET NO TYPES</option> 218 <option value="SUPERSET_NO_TYPES">SUPERSET NO TYPES</option>
223 <option value="SUBSET" selected="True">SUBSET</option> 219 <option value="SUBSET" selected="True">SUBSET</option>
224 <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option> 220 <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option>
225 <option value="ONE">ONE</option> 221 <option value="ONE">ONE</option>
226 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option> 222 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>
223 <option value="ACCESSION">ACCESSION</option>
227 </param> 224 </param>
228 225
229 <param name="proteoform_peptideshakerzip_range" type="integer" value="0" label="Integer range of error for PTM sites" optional="true" 226 <param name="proteoform_peptideshakerzip_range" type="integer" value="0" label="Integer range of error for PTM sites" optional="true"
230 help="Plus minus positions for the same PTM site"/> 227 help="Plus minus positions for the same PTM site"/>
231 </when> 228 </when>
293 <option value="SUPERSET_NO_TYPES">SUPERSET NO TYPES</option> 290 <option value="SUPERSET_NO_TYPES">SUPERSET NO TYPES</option>
294 <option value="SUBSET" selected="True">SUBSET</option> 291 <option value="SUBSET" selected="True">SUBSET</option>
295 <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option> 292 <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option>
296 <option value="ONE">ONE</option> 293 <option value="ONE">ONE</option>
297 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option> 294 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>
295 <option value="ACCESSION">ACCESSION</option>
298 </param> 296 </param>
299 297
300 <param name="modifiedpeptide_ptm_range" type="integer" value="0" label="PTM position range" optional="true" 298 <param name="modifiedpeptide_ptm_range" type="integer" value="0" label="PTM position range" optional="true"
301 help="Integer number margin error for sites of PTMs. Only for modified peptides."/> 299 help="Integer number margin error for sites of PTMs. Only for modified peptides."/>
302 </when> 300 </when>
303
304
305 301
306 </conditional> 302 </conditional>
307 303
308 </repeat> 304 </repeat>
309 305
343 <conditional name="match_type"> 339 <conditional name="match_type">
344 <param name="match_type_selector" value="gene"/> 340 <param name="match_type_selector" value="gene"/>
345 <param name="input_gene" value="genes.txt" ftype="txt" /> 341 <param name="input_gene" value="genes.txt" ftype="txt" />
346 </conditional> 342 </conditional>
347 </repeat> 343 </repeat>
348 <output name="search" file="genes_search.tsv" ftype="tsv" compare="sim_size" delta="3000" /> 344 <output name="search" ftype="tsv" >
345 <assert_contents>
346 <has_line_matching expression="CFTR\tP13569\tR-HSA-383190\tHCO3- transport through ion channel\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules"/>
347 <has_line_matching expression="TGFB1\tP01137\tR-HSA-170850\tPhosphorylated SMAD2/3 dissociates from TGFBR\tR-HSA-170834\tSignaling by TGF-beta Receptor Complex\tR-HSA-162582\tSignal Transduction"/>
348 <has_line_matching expression="SCNN1B\tP51168\tR-HSA-2682349\tRAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules"/>
349 <has_line_matching expression="TNFRSF1A\tP19438\tR-HSA-5626988\tTNF-alpha:TNFR1 binds NSMAF\tR-HSA-75893\tTNF signaling\tR-HSA-162582\tSignal Transduction"/>
350 <has_n_columns n="8" />
351 </assert_contents>
352 </output>
349 </test> 353 </test>
350 354
351 <!-- Test graphs from proteoforms --> 355 <!-- Test graphs from proteoforms -->
352 <test> 356 <test>
353 <repeat name="match_types"> 357 <repeat name="match_types">
357 <param name="proteoform_match_criteria" value="SUBSET"/> 361 <param name="proteoform_match_criteria" value="SUBSET"/>
358 </conditional> 362 </conditional>
359 </repeat> 363 </repeat>
360 <param name="output_graphs" value="gg,gu,gp" /> 364 <param name="output_graphs" value="gg,gu,gp" />
361 <output_collection name="graphs_files" type="list"> 365 <output_collection name="graphs_files" type="list">
362 <!-- <element name="geneExternalEdges" ftype="tsv" file="proteoforms_graphs/geneExternalEdges.tsv" compare="sim_size" delta="1000" /> --> 366 <element name="geneExternalEdges" ftype="tsv">
363 <element name="geneInternalEdges" ftype="tsv" file="proteoforms_graphs/geneInternalEdges.tsv" compare="sim_size" delta="1000"/> 367 <assert_contents>
364 <element name="geneVertices" ftype="tsv" file="proteoforms_graphs/geneVertices.tsv" compare="sim_size" delta="1000"/> 368 <has_line_matching expression="ERBB4\tSRC\tReaction\tR-HSA-1963586\tcatalyst\tcatalyst"/>
365 <element name="proteinExternalEdges" ftype="tsv" file="proteoforms_graphs/proteinExternalEdges.tsv" compare="sim_size" delta="10000"/> 369 <has_line_matching expression="RNF85\tSRC1\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst"/>
366 <element name="proteinInternalEdges" ftype="tsv" file="proteoforms_graphs/proteinInternalEdges.tsv" compare="sim_size" delta="1000"/> 370 <has_line_matching expression="CBL2\tUNQ2500/PRO5800\tReaction\tR-HSA-5654677\tinput\tinput"/>
367 <element name="proteinVertices" ftype="tsv" file="proteoforms_graphs/proteinVertices.tsv" compare="sim_size" delta="1000"/> 371 <has_line_matching expression="FN1\tPRKM3\tReaction\tR-HSA-5672973\tcatalyst\toutput"/>
368 <element name="proteoformExternalEdges" ftype="tsv" file="proteoforms_graphs/proteoformExternalEdges.tsv" compare="sim_size" delta="1000"/> 372 <has_line_matching expression="MAPK11\tMAPK12\tSet\tR-HSA-448855\tmember/candidate\tmember/candidate"/>
369 <element name="proteoformInternalEdges" ftype="tsv" file="proteoforms_graphs/proteoformInternalEdges.tsv" compare="sim_size" delta="1000"/> 373 <has_line_matching expression="SAPK2B\tSAPK3\tSet\tR-HSA-448855\tmember/candidate\tmember/candidate"/>
370 <element name="proteoformVertices" ftype="tsv" file="proteoforms_graphs/proteoformVertices.tsv" compare="sim_size" delta="1000"/> 374 <has_n_columns n="6" />
375 </assert_contents>
376 </element>
377 <element name="geneInternalEdges" ftype="tsv" file="proteoforms_graphs/geneInternalEdges.tsv" compare="sim_size" delta="10"/>
378 <element name="geneVertices" ftype="tsv">
379 <assert_contents>
380 <has_line_matching expression="ERK1\tMitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber"/>
381 <has_line_matching expression="CREB1\tCyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ]"/>
382 <has_line_matching expression="SAPK2\tMitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber"/>
383 <has_line_matching expression="STAT5\tSignal transducer and activator of transcription 5A ]"/>
384 <has_n_columns n="2" />
385 </assert_contents>
386 </element>
387 <element name="proteinExternalEdges" ftype="tsv">
388 <assert_contents>
389 <has_line_matching expression="P12931\tP56975\tReaction\tR-HSA-1963586\tcatalyst\toutput"/>
390 <has_line_matching expression="P12931\tP51617\tReaction\tR-HSA-2316434\tcatalyst\tregulator"/>
391 <has_line_matching expression="P12931\tQ8N302\tReaction\tR-HSA-6802933\tcatalyst\tinput"/>
392 <has_line_matching expression="O95352\tP12931\tComplex\tR-HSA-6802695\tcomponent\tcomponent"/>
393 <has_line_matching expression="Q15759\tQ16539\tSet\tR-HSA-198703\tmember/candidate\tmember/candidate"/>
394 <has_n_columns n="6" />
395 </assert_contents>
396 </element>
397 <element name="proteinInternalEdges" ftype="tsv">
398 <assert_contents>
399 <has_line_matching expression="P00519\tP12931\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst"/>
400 <has_line_matching expression="P12931\tQ9UQC2\tReaction\tR-HSA-205234\toutput\toutput"/>
401 <has_line_matching expression="P12931\tP27361\tReaction\tR-HSA-6802933\tinput\toutput"/>
402 <has_line_matching expression="P12931\tP27361\tReaction\tR-HSA-6802910\tinput\tinput"/>
403 <has_line_matching expression="P00519\tP12931\tSet\tR-HSA-8942611\tmember/candidate\tmember/candidate"/>
404 <has_line_matching expression="P12931\tP42229\tComplex\tR-HSA-1469999\tcomponent\tcomponent"/>
405 <has_n_columns n="6" />
406 </assert_contents>
407 </element>
408 <element name="proteinVertices" ftype="tsv">
409 <assert_contents>
410 <has_line_matching expression="P16220\tCyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ]"/>
411 <has_line_matching expression="P27361\tMitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber"/>
412 <has_line_matching expression="P42229\tSignal transducer and activator of transcription 5A ]"/>
413 <has_n_columns n="2" />
414 </assert_contents>
415 </element>
416 <element name="proteoformExternalEdges" ftype="tsv">
417 <assert_contents>
418 <has_line_matching expression="O43597;00048:55,00048:227\tP22681;\tComplex\tR-HSA-934576\tcomponent\tcomponent"/>
419 <has_line_matching expression="P00533;00048:992,00048:1045,00048:1068,00048:1086,00048:1148,00048:1173\tP22681;\tComplex\tR-HSA-182935\tcomponent\tcomponent"/>
420 <has_line_matching expression="P27361;00047:202,00048:204\tP28482;00047:185,00048:187\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate"/>
421 <has_line_matching expression="P12931;00048:419\tQ01196;\tComplex\tR-HSA-8937687\tcomponent\tcomponent"/>
422 <has_line_matching expression="P15509;\tP42229;00048:694\tSet\tR-HSA-913465\tmember/candidate\tmember/candidate"/>
423 <has_n_columns n="6" />
424 </assert_contents>
425 </element>
426 <element name="proteoformInternalEdges" ftype="tsv">
427 <assert_contents>
428 <has_line_matching expression="P27361;00047:202,00048:204\tQ15759;00047:180,00048:182\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate"/>
429 <has_line_matching expression="P27361;00047:202,00048:204\tQ15759;00047:180,00048:182\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate"/>
430 <has_n_columns n="6" />
431 </assert_contents>
432 </element>
433 <element name="proteoformVertices" ftype="tsv">
434 <assert_contents>
435 <has_line_matching expression="P16220;00046:133\tCyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ]"/>
436 <has_line_matching expression="Q15759;00047:180,00048:182\tMitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber"/>
437 <has_line_matching expression="P42229;00048:694\tSignal transducer and activator of transcription 5A ]"/>
438 <has_n_columns n="2" />
439 </assert_contents>
440 </element>
441
371 </output_collection> 442 </output_collection>
372 </test> 443 </test>
373 444
374 </tests> 445 </tests>
375 <help> 446 <help>
416 487
417 .. class:: infomark 488 .. class:: infomark
418 489
419 **Try it now** 490 **Try it now**
420 491
421 You can easily test PathwayMatcher functionality using the example files we provide with proteoforms and proteins information of Cystic Fibrosis: 492 You can easily test PathwayMatcher functionality creating text files with the example data we provide with proteoforms and proteins information of Cystic Fibrosis:
422 493
423 https://media.githubusercontent.com/media/PathwayAnalysisPlatform/PathwayMatcher/master/src/test/resources/Proteoforms/Simple/CysticFibrosis.txt 494 **Proteoforms**:
424 495
425 https://media.githubusercontent.com/media/PathwayAnalysisPlatform/PathwayMatcher/master/src/test/resources/Proteins/UniProt/CysticFibrosis.txt 496 ::
426 497
427 You can upload them to Galaxy by directly copying and pasting their URL into the Galaxy upload dialog (the button with the arrow pointing up in the top-left area, and then choosing *Pasta/Fetch data*). 498 P01137;
499 P10145;
500 P12318;
501 P12318;00048:288,00048:304
502 P13569;
503 P13569;01148:null
504 P19438;
505 P37088;
506 P37088;01148:null
507 P51168;
508 P51170;
509 P51170;01148:null
510 Q14CN2;
511 Q16623;
512 Q9UJW0;
513
514 **Proteins**:
515 ::
516
517 P13569
518 P01137
519 P12318
520 Q9UJW0
521 P51168
522 P51170
523 P37088
524 P19438
525 Q14CN2
526 Q16623
527 P10145
528
529 After copying and pasting this data into new text files, you can upload them to Galaxy by directly using the Galaxy upload dialog (the button with the arrow pointing up in the top-left area, and then choosing *Choose local file*).
428 530
429 Once they appear in green in your history, they have been uploaded and you can use them as inputs in PathwayMatcher. 531 Once they appear in green in your history, they have been uploaded and you can use them as inputs in PathwayMatcher.
430 532
431 Now, select *Proteoforms* as input type and, in the next drop-down list, the entry of your history corresponding to the proteoforms file you uploaded. 533 Now, select *Proteoforms* as input type and, in the next drop-down list, the entry of your history corresponding to the proteoforms file you uploaded.
432 534
460 562
461 [6] The PSI-MOD community standard for representation of protein modification data. Nature Biotechnology 26, 864 - 866 (2008): 563 [6] The PSI-MOD community standard for representation of protein modification data. Nature Biotechnology 26, 864 - 866 (2008):
462 http://www.nature.com/nbt/journal/v26/n8/full/nbt0808-864.html 564 http://www.nature.com/nbt/journal/v26/n8/full/nbt0808-864.html
463 565
464 .. _dbSNP: https://www.ncbi.nlm.nih.gov/projects/SNP/ 566 .. _dbSNP: https://www.ncbi.nlm.nih.gov/projects/SNP/
465 .. _PathwayMatcher: https://github.com/LuisFranciscoHS/PathwayMatcher 567 .. _PathwayMatcher: https://github.com/PathwayAnalysisPlatform/PathwayMatcher
466 .. _Input: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Input 568 .. _Input: https://github.com/PathwayAnalysisPlatform/PathwayMatcher/wiki/Input
467 .. _Output: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Output 569 .. _Output: https://github.com/PathwayAnalysisPlatform/PathwayMatcher/wiki/Output
468 570
469 </help> 571 </help>
470 572
471 <citations> 573 <citations>
472 <citation type="doi">doi:10.1101/375097</citation> 574 <citation type="doi">doi:10.1101/375097</citation>