Mercurial > repos > iracooke > msgfplus
annotate msgfplus_search.xml @ 16:66a149ef79f7 draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 20:01:47 -0400 |
| parents | 6c751c59ce18 |
| children | 7990ee72821b |
| rev | line source |
|---|---|
| 15 | 1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0"> |
| 10 | 2 <description>Run an MSGF+ Search</description> |
| 3 <requirements> | |
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66a149ef79f7
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
15
diff
changeset
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4 <container type="docker">iracooke/protk-1.4.3</container> |
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66a149ef79f7
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
15
diff
changeset
|
5 <requirement type="package" version="1.4.3">protk</requirement> |
| 10 | 6 <requirement type="package" version="20140210">msgfplus</requirement> |
| 7 <requirement type="package" version="3_0_4388">proteowizard</requirement> | |
| 8 </requirements> | |
| 9 <command> | |
| 10 msgfplus_search.rb | |
| 11 #if $database.source_select=="built_in": | |
| 12 --galaxy -d $database.dbkey | |
| 13 #else | |
| 14 --galaxy -d $database.fasta_file | |
| 15 #end if | |
| 16 | |
| 17 --var-mods=' | |
| 18 $variable_mods | |
| 19 #for $custom_variable_mod in $custom_variable_mods: | |
| 20 ,${custom_variable_mod.custom_mod} | |
| 21 #end for | |
| 22 ' | |
| 23 | |
| 24 --fix-mods=' | |
| 25 $fixed_mods | |
| 26 #for $custom_fix_mod in $custom_fix_mods: | |
| 27 ,${custom_fix_mod.custom_mod} | |
| 28 #end for | |
| 29 ' | |
| 30 | |
| 31 $input_file | |
| 32 -o $output | |
| 33 -r | |
| 34 --enzyme=$enzyme | |
| 35 --precursor-ion-tol-units=$precursor_tolu | |
| 36 -v $missed_cleavages | |
| 37 $cleavage_semi | |
| 38 -p $precursor_ion_tol | |
| 39 --instrument=$instrument | |
| 40 --isotope-error-range=$isotope_error_range | |
| 41 --fragment-method=$fragment_method | |
| 42 --protocol=$protocol | |
| 43 --min-pep-len=$min_pep_len | |
| 44 --max-pep-len=$max_pep_len | |
| 45 --max-pep-charge=$max_pep_charge | |
| 46 --min-pep-charge=$min_pep_charge | |
| 47 --num-reported-matches=$num_reported_matches | |
| 48 --java-mem=$java_mem | |
| 15 | 49 |
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16
66a149ef79f7
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
15
diff
changeset
|
50 --threads "\${GALAXY_SLOTS:-12}" |
| 12 | 51 #if $pepxml_output_use: |
| 52 --pepxml | |
| 13 | 53 #end if |
| 10 | 54 </command> |
| 55 | |
| 56 <inputs> | |
| 57 <conditional name="database"> | |
| 58 <param name="source_select" type="select" label="Database source"> | |
| 59 <option value="built_in">Built-In</option> | |
| 60 <option value="input_ref" selected="true">Your Upload File</option> | |
| 61 </param> | |
| 62 <when value="built_in"> | |
| 63 <param name="dbkey" type="select" format="text" > | |
| 64 <label>Database</label> | |
| 65 <options from_file="pepxml_databases.loc"> | |
| 66 <column name="name" index="0" /> | |
| 67 <column name="value" index="2" /> | |
| 68 </options> | |
| 69 </param> | |
| 70 </when> | |
| 71 <when value="input_ref"> | |
| 72 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> | |
| 73 </when> | |
| 74 </conditional> | |
| 14 | 75 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/> |
| 10 | 76 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed"> |
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16
66a149ef79f7
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
15
diff
changeset
|
77 <options from_file="msgfplus_mods_var.loc"> |
| 10 | 78 <column name="name" index="0" /> |
| 79 <column name="value" index="2" /> | |
| 80 </options> | |
| 81 </param> | |
| 82 <repeat name="custom_variable_mods" title="Custom Variable Modifications" | |
| 83 help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these"> | |
| 84 <param name="custom_mod" type="text" /> | |
| 85 </repeat> | |
| 86 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed"> | |
|
16
66a149ef79f7
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
15
diff
changeset
|
87 <options from_file="msgfplus_mods_fix.loc"> |
| 10 | 88 <column name="name" index="0" /> |
| 89 <column name="value" index="2" /> | |
| 90 </options> | |
| 91 </param> | |
| 92 <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these"> | |
| 93 <param name="custom_mod" type="text"> | |
| 94 </param> | |
| 95 </repeat> | |
| 96 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites"> | |
| 97 <label>Missed Cleavages Allowed</label> | |
| 98 <option value="0">0</option> | |
| 99 <option value="1">1</option> | |
| 15 | 100 <option selected="true" value="2">2</option> |
| 10 | 101 </param> |
| 102 | |
| 11 | 103 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue="" /> |
| 10 | 104 |
| 105 <param name="enzyme" type="select" format="text"> | |
| 106 <label>Enzyme</label> | |
| 107 <option value="0">unspecific cleavage</option> | |
| 12 | 108 <option value="1" selected="true">Trypsin</option> |
| 10 | 109 <option value="2">Chymotrypsin</option> |
| 110 <option value="3">Lys-C</option> | |
| 111 <option value="4">Lys-N</option> | |
| 112 <option value="5">glutamyl endopeptidase</option> | |
| 113 <option value="6">Arg-C</option> | |
| 114 <option value="7">Asp-N</option> | |
| 115 <option value="8">alphaLP</option> | |
| 116 <option value="9">no cleavage</option> | |
| 117 </param> | |
| 118 | |
| 119 <param name="instrument" type="select" format="text"> | |
| 120 <label>Instrument Type</label> | |
| 121 <option value="2">TOF</option> | |
| 15 | 122 <option value="0" selected="true">Low-res LCQ/LTQ</option> |
| 10 | 123 <option value="1">High-res LTQ</option> |
| 124 </param> | |
| 125 | |
| 126 <param name="fragment_method" type="select" format="text"> | |
| 127 <label>Fragmentation Method</label> | |
| 128 <option value="0">Respect Input File</option> | |
| 129 <option value="1">CID</option> | |
| 130 <option value="2">ETD</option> | |
| 131 <option value="3">HCD</option> | |
| 132 <option value="4">Merge spectra from same precursor</option> | |
| 133 </param> | |
| 134 | |
| 135 <param name="protocol" type="select" format="text"> | |
| 136 <label>Protocol</label> | |
| 137 <option value="0">NoProtocol</option> | |
| 138 <option value="1">Phosphorylation</option> | |
| 139 <option value="2">iTRAQ</option> | |
| 140 <option value="3">iTRAQPhospho</option> | |
| 141 </param> | |
| 142 | |
| 15 | 143 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/> |
| 10 | 144 <param name="precursor_tolu" type="select" format="text"> |
| 145 <label>Precursor Ion Tolerance Units</label> | |
| 146 <option value="ppm">ppm</option> | |
| 147 <option value="Da">Da</option> | |
| 148 </param> | |
| 149 | |
| 150 <param name="isotope_error_range" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation." type="text" size="80" value="0,1" label="Isotope Error Range"/> | |
| 151 <param name="min_pep_len" help="" type="integer" value="6" label="Minimum Peptide Length"/> | |
| 152 <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/> | |
| 153 <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/> | |
| 154 <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/> | |
| 155 <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/> | |
| 156 <param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/> | |
| 15 | 157 <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" /> |
| 10 | 158 </inputs> |
| 159 <outputs> | |
| 15 | 160 <data format="mzid" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.${'pepXML' if $pepxml_output_use else 'mzid'}"> |
| 10 | 161 <change_format> |
| 15 | 162 <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file"/> |
| 10 | 163 </change_format> |
| 164 </data> | |
| 165 </outputs> | |
| 15 | 166 |
| 10 | 167 <tests> |
| 15 | 168 <!-- Just test that the tool runs and produces vaguely correct output --> |
| 10 | 169 <test> |
| 170 <param name="source_select" value="input_ref"/> | |
| 15 | 171 <param name="fasta_file" value="testdb.fasta" format="fasta"/> |
| 172 <param name="input_file" value="tiny.mzML" format="mzml"/> | |
| 173 <param name="precursor_ion_tol" value="200"/> | |
| 174 <param name="pepxml_output_use" value="true"/> | |
| 175 <output name="output" format="raw_pepxml"> | |
| 176 <assert_contents> | |
| 177 <has_text text="FALPQYLKTVYQHQKAMKPWIQPKTKVIPYVRYL" /> | |
| 178 </assert_contents> | |
| 179 </output> | |
| 10 | 180 </test> |
| 181 </tests> | |
| 15 | 182 |
| 10 | 183 <help> |
| 184 | |
| 185 **What it does** | |
| 186 | |
| 187 Runs an MS/MS database search using the MSGFPlus search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores. | |
| 188 | |
| 189 ---- | |
| 190 | |
| 191 **References** | |
| 192 | |
| 193 Please see http://proteomics.ucsd.edu/Software/MSGFPlus.html for details of the MSGFPlus search engine and references describing its algorithm | |
| 194 | |
| 195 </help> | |
| 196 </tool> |