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comparison morpheus.xml @ 1:ecb9ec15083d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999
author galaxyp
date Thu, 15 Dec 2016 17:41:50 -0500
parents 553f0336e43e
children e0104a9f20f0
comparison
equal deleted inserted replaced
0:553f0336e43e 1:ecb9ec15083d
39 <expand macro="modification_options"/> 39 <expand macro="modification_options"/>
40 </xml> 40 </xml>
41 </macros> 41 </macros>
42 42
43 <requirements> 43 <requirements>
44 <requirement version="4.0">mono</requirement> 44 <requirement type="package" version="255">morpheus</requirement>
45 <requirement version="255">morpheus</requirement>
46 </requirements> 45 </requirements>
47 46
48 <stdio> 47 <stdio>
49 <exit_code range="1:" /> 48 <exit_code range="1:" />
50 <regex match="System..*Exception" 49 <regex match="System..*Exception"
53 description="Error encountered" /> 52 description="Error encountered" />
54 </stdio> 53 </stdio>
55 54
56 <command><![CDATA[ 55 <command><![CDATA[
57 mkdir -p output_reports && 56 mkdir -p output_reports &&
58 cwd=`pwd`&& 57 cwd=`pwd` &&
59 #import re 58 #import re
60 #set $searchdb_name = $searchdb 59 #set $searchdb_name = $searchdb
61 #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension('uniprotxml').__class__): 60 #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension('uniprotxml').__class__):
62 #set $searchdb_name = 'searchdb.xml' 61 #set $searchdb_name = 'searchdb.xml'
63 #else 62 #else
73 #end if 72 #end if
74 #set $input_list = $input_list + [$input_name] 73 #set $input_list = $input_list + [$input_name]
75 && ln -s $input $input_name 74 && ln -s $input $input_name
76 #end for 75 #end for
77 #set $input_names = ','.join($input_list) 76 #set $input_names = ','.join($input_list)
78 && mono \${MORPHEUS_PATH}/morpheus_mzml_mono_cl.exe 77 &&
79 -d="$input_names" 78
80 -db=$searchdb_name 79 mono `which morpheus`
80 -d='$input_names'
81 -db='$searchdb_name'
82
81 #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension('uniprotxml').__class__): 83 #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension('uniprotxml').__class__):
82 #if str( $advanced.adv_options_selector) == "set": 84 #if str( $advanced.adv_options_selector) == "set":
83 $advanced.noup 85 $advanced.noup
84 #end if 86 #end if
85 #end if 87 #end if
230 <data name="output_psms" format="tabular" label="${tool.name} on ${on_string}: PSMs.tsv" from_work_dir="output_reports/aggregate.PSMs.tsv" /> 232 <data name="output_psms" format="tabular" label="${tool.name} on ${on_string}: PSMs.tsv" from_work_dir="output_reports/aggregate.PSMs.tsv" />
231 <data name="output_unique_peptides" format="tabular" label="${tool.name} on ${on_string}: unique_peptides.tsv" from_work_dir="output_reports/aggregate.unique_peptides.tsv" /> 233 <data name="output_unique_peptides" format="tabular" label="${tool.name} on ${on_string}: unique_peptides.tsv" from_work_dir="output_reports/aggregate.unique_peptides.tsv" />
232 <data name="output_protein_groups" format="tabular" label="${tool.name} on ${on_string}: protein_groups.tsv" from_work_dir="output_reports/aggregate.protein_groups.tsv" /> 234 <data name="output_protein_groups" format="tabular" label="${tool.name} on ${on_string}: protein_groups.tsv" from_work_dir="output_reports/aggregate.protein_groups.tsv" />
233 <data name="aggregate_mzid" format="mzid" label="${tool.name} on ${on_string}: aggregate.mzid" from_work_dir="output_reports/aggregate.mzid" /> 235 <data name="aggregate_mzid" format="mzid" label="${tool.name} on ${on_string}: aggregate.mzid" from_work_dir="output_reports/aggregate.mzid" />
234 <collection name="morpheus_pep_xmls" type="list" label="${tool.name} on ${on_string} pep.xml"> 236 <collection name="morpheus_pep_xmls" type="list" label="${tool.name} on ${on_string} pep.xml">
235 <discover_datasets pattern="(?P&lt;name&gt;.*\.pep.xml)" ext="pepxml" visible="False" directory="output_reports" /> 237 <discover_datasets pattern="(?P&lt;name&gt;.*\.pep.xml)" ext="pepxml" visible="false" directory="output_reports" />
236 </collection> 238 </collection>
237 </outputs> 239 </outputs>
238 <tests> 240 <tests>
239 <test> 241 <test>
240 <param name="input" value="test_input.mzML" ftype="mzml"/> 242 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
241 <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/> 243 <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
242 <param name="fdr" value="1"/> 244 <param name="fdr" value="1"/>
243 <param name="mvmi" value="1024"/> 245 <param name="mvmi" value="1024"/>
244 <param name="precmt" value="Monoisotopic"/> 246 <param name="precmt" value="Monoisotopic"/>
245 <param name="precmtu" value="Da"/> 247 <param name="precmtu" value="Da"/>
246 <param name="precmtv" value="2.5"/> 248 <param name="precmtv" value="2.5"/>
247 <output name="output_psms"> 249 <output name="output_psms">
248 <assert_contents> 250 <assert_contents>
249 <has_text text="K.TTGSSSSSSSK.K" /> 251 <not_has_text text="K.TTGSSSSSSSK.K" />
250 <not_has_text text="carbamidomethylation of C" /> 252 <has_text text="carbamidomethylation of C" />
251 <not_has_text text="(oxidation of M)" /> 253 <has_text text="(oxidation of M)" />
252 </assert_contents> 254 </assert_contents>
253 </output> 255 </output>
254 </test> 256 </test>
255 <test> 257 <test>
256 <param name="input" value="test_input.mzML" ftype="mzml"/> 258 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
257 <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/> 259 <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
258 <param name="fdr" value="1"/> 260 <param name="fdr" value="1"/>
259 <param name="mvmi" value="1024"/> 261 <param name="mvmi" value="1024"/>
260 <param name="precmt" value="Monoisotopic"/> 262 <param name="precmt" value="Monoisotopic"/>
261 <param name="precmtu" value="Da"/> 263 <param name="precmtu" value="Da"/>
268 <not_has_text text="K.TTGSSSSSSSK.K" /> 270 <not_has_text text="K.TTGSSSSSSSK.K" />
269 </assert_contents> 271 </assert_contents>
270 </output> 272 </output>
271 </test> 273 </test>
272 <test> 274 <test>
273 <param name="input" value="test_input.mzML" ftype="mzml"/> 275 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
274 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/> 276 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
275 <param name="fdr" value="1"/> 277 <param name="fdr" value="1"/>
276 <param name="mvmi" value="1024"/> 278 <param name="mvmi" value="1024"/>
277 <param name="precmt" value="Monoisotopic"/> 279 <param name="precmt" value="Monoisotopic"/>
278 <param name="precmtu" value="Da"/> 280 <param name="precmtu" value="Da"/>
285 <not_has_text text="K.KYFLENKIGTDR.R" /> 287 <not_has_text text="K.KYFLENKIGTDR.R" />
286 </assert_contents> 288 </assert_contents>
287 </output> 289 </output>
288 </test> 290 </test>
289 <test> 291 <test>
290 <param name="input" value="test_input.mzML" ftype="mzml"/> 292 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
291 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/> 293 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
292 <param name="fdr" value="1"/> 294 <param name="fdr" value="1"/>
293 <param name="mvmi" value="1024"/> 295 <param name="mvmi" value="1024"/>
294 <param name="precmt" value="Monoisotopic"/> 296 <param name="precmt" value="Monoisotopic"/>
295 <param name="precmtu" value="Da"/> 297 <param name="precmtu" value="Da"/>