comparison msgfplus_search.xml @ 16:66a149ef79f7 draft

planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty

15:6c751c59ce18

<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0">
    <description>Run an MSGF+ Search</description>
    <requirements>
        <container type="docker">iracooke/protk-1.4.1</container>
        <requirement type="package" version="1.4">protk</requirement>
        <requirement type="package" version="20140210">msgfplus</requirement>
        <requirement type="package" version="3_0_4388">proteowizard</requirement>
    </requirements>
    <command>
        msgfplus_search.rb

        --max-pep-charge=$max_pep_charge
        --min-pep-charge=$min_pep_charge
        --num-reported-matches=$num_reported_matches
        --java-mem=$java_mem

        --threads $threads

        #if $pepxml_output_use:
        --pepxml
        #end if
    </command>

                <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
            </when>
        </conditional>
        <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
        <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
            <options from_file="msgfplus_mods.loc">
                <column name="name" index="0" />
                <column name="value" index="2" />
            </options>
        </param>
        <repeat name="custom_variable_mods" title="Custom Variable Modifications" 
            help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
            <param name="custom_mod" type="text" />
        </repeat>
        <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed">
            <options from_file="msgfplus_mods.loc">
                <column name="name" index="0" />
                <column name="value" index="2" />
            </options>
        </param>
        <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">

        <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/>
        <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/>
        <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
        <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
        <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"/>
        <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search."/>        
        <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
    </inputs>
    <outputs>
        <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'}">
            <change_format>

16:66a149ef79f7

<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0">
    <description>Run an MSGF+ Search</description>
    <requirements>
        <container type="docker">iracooke/protk-1.4.3</container>
        <requirement type="package" version="1.4.3">protk</requirement>
        <requirement type="package" version="20140210">msgfplus</requirement>
        <requirement type="package" version="3_0_4388">proteowizard</requirement>
    </requirements>
    <command>
        msgfplus_search.rb

        --max-pep-charge=$max_pep_charge
        --min-pep-charge=$min_pep_charge
        --num-reported-matches=$num_reported_matches
        --java-mem=$java_mem

        --threads "\${GALAXY_SLOTS:-12}"
        #if $pepxml_output_use:
        --pepxml
        #end if
    </command>

                <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
            </when>
        </conditional>
        <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
        <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
            <options from_file="msgfplus_mods_var.loc">
                <column name="name" index="0" />
                <column name="value" index="2" />
            </options>
        </param>
        <repeat name="custom_variable_mods" title="Custom Variable Modifications" 
            help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
            <param name="custom_mod" type="text" />
        </repeat>
        <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed">
            <options from_file="msgfplus_mods_fix.loc">
                <column name="name" index="0" />
                <column name="value" index="2" />
            </options>
        </param>
        <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">

        <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/>
        <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/>
        <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
        <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
        <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"/>
        <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
    </inputs>
    <outputs>
        <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'}">
            <change_format>