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comparison msgfplus_search.xml @ 16:66a149ef79f7 draft

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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
comparison
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15:6c751c59ce18 16:66a149ef79f7
1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0"> 1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0">
2 <description>Run an MSGF+ Search</description> 2 <description>Run an MSGF+ Search</description>
3 <requirements> 3 <requirements>
4 <container type="docker">iracooke/protk-1.4.1</container> 4 <container type="docker">iracooke/protk-1.4.3</container>
5 <requirement type="package" version="1.4">protk</requirement> 5 <requirement type="package" version="1.4.3">protk</requirement>
6 <requirement type="package" version="20140210">msgfplus</requirement> 6 <requirement type="package" version="20140210">msgfplus</requirement>
7 <requirement type="package" version="3_0_4388">proteowizard</requirement> 7 <requirement type="package" version="3_0_4388">proteowizard</requirement>
8 </requirements> 8 </requirements>
9 <command> 9 <command>
10 msgfplus_search.rb 10 msgfplus_search.rb
45 --max-pep-charge=$max_pep_charge 45 --max-pep-charge=$max_pep_charge
46 --min-pep-charge=$min_pep_charge 46 --min-pep-charge=$min_pep_charge
47 --num-reported-matches=$num_reported_matches 47 --num-reported-matches=$num_reported_matches
48 --java-mem=$java_mem 48 --java-mem=$java_mem
49 49
50 --threads $threads 50 --threads "\${GALAXY_SLOTS:-12}"
51
52 #if $pepxml_output_use: 51 #if $pepxml_output_use:
53 --pepxml 52 --pepxml
54 #end if 53 #end if
55 </command> 54 </command>
56 55
73 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> 72 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
74 </when> 73 </when>
75 </conditional> 74 </conditional>
76 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/> 75 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
77 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed"> 76 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
78 <options from_file="msgfplus_mods.loc"> 77 <options from_file="msgfplus_mods_var.loc">
79 <column name="name" index="0" /> 78 <column name="name" index="0" />
80 <column name="value" index="2" /> 79 <column name="value" index="2" />
81 </options> 80 </options>
82 </param> 81 </param>
83 <repeat name="custom_variable_mods" title="Custom Variable Modifications" 82 <repeat name="custom_variable_mods" title="Custom Variable Modifications"
84 help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these"> 83 help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
85 <param name="custom_mod" type="text" /> 84 <param name="custom_mod" type="text" />
86 </repeat> 85 </repeat>
87 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed"> 86 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed">
88 <options from_file="msgfplus_mods.loc"> 87 <options from_file="msgfplus_mods_fix.loc">
89 <column name="name" index="0" /> 88 <column name="name" index="0" />
90 <column name="value" index="2" /> 89 <column name="value" index="2" />
91 </options> 90 </options>
92 </param> 91 </param>
93 <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"> 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">
153 <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/> 152 <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/>
154 <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/> 153 <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/>
155 <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/> 154 <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
156 <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/> 155 <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
157 <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"/> 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"/>
158 <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search."/>
159 <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" /> 157 <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
160 </inputs> 158 </inputs>
161 <outputs> 159 <outputs>
162 <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 $pepxml_output_use else 'mzid'}"> 160 <data format="mzid" name="output" metadata_source="input_file" label="MSGF+_vs_${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'}">
163 <change_format> 161 <change_format>