comparison msgfplus_search.xml @ 9:827f19088303 draft default tip

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

8:dfb2b78b3aff

<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.3">
    <description>Run an MSGF+ Search</description>
    <requirements>
        <container type="docker">simonalpha/protk:1.4.0</container>
        <requirement type="package" version="1.3">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 $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>
                <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="source_select" value="input_ref"/>
              <param name="fasta_file" value="bsa.fasta"/>
                  <param name="input_file" value="bsa.mzML"/>
              <output name="output" file="bsa.mzid" compare="sim_size" delta="600" /> 
        </test>
    </tests>
    <help>

**What it does**

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.

9:827f19088303

<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>
                <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file"/>
            </change_format>
        </data>
    </outputs>

    <tests>
        <!-- Just test that the tool runs and produces vaguely correct output -->
        <test>
            <param name="source_select" value="input_ref"/>
            <param name="fasta_file" value="testdb.fasta" format="fasta"/>
            <param name="input_file" value="tiny.mzML" format="mzml"/>
            <param name="precursor_ion_tol" value="200"/>
            <param name="pepxml_output_use" value="true"/>
            <output name="output" format="raw_pepxml">
                <assert_contents>
                    <has_text text="FALPQYLKTVYQHQKAMKPWIQPKTKVIPYVRYL" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help>

**What it does**

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.