annotate filter_psms.xml @ 3:86fd1757f102 draft default tip

planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98

<tool id="filter_psms" name="Filter PSMs" version="1.0.0">
	<description>Select PSMs in a pepXML file matching criteria</description>

	<requirements>
	    <requirement type="package" version="1.4">protk</requirement>
   </requirements>

	<command>
		filter_psms.rb 

		'
		$first_expression
    #for $expression in $expressions:
    ,${expression.expression}
    #end for
    '

    $pepxml_file

    --attribute $attribute

    $check_alt

    $reverse

		-o $output


	</command>

	<stdio>
		<exit_code range="1:"   level="fatal"   description="Failure" />
	</stdio>

	<inputs>	

		<param name="pepxml_file" type="data" format="pepxml,raw_pepxml" multiple="false" label="Proteomics Search Results" help="A pepXML file"/>


        <param name="first_expression" type="text" size="40" value="decoy_" label="Expression">
	    	<sanitizer>
        	<valid initial="string.printable">
         	<remove value="&apos;"/>
        	</valid>
        	<mapping initial="none">
          	<add source="&apos;" target="__sq__"/>
        	</mapping>
      		</sanitizer>            	
        </param>

        <repeat name="expressions" title="Expressions to Match against" help="These can include regular expressions">
            <param name="expression" type="text" size="40" value="decoy_" label="Expression">
		    	<sanitizer>
	        	<valid initial="string.printable">
	         	<remove value="&apos;"/>
	        	</valid>
	        	<mapping initial="none">
	          	<add source="&apos;" target="__sq__"/>
	        	</mapping>
	      		</sanitizer>            	
            </param>
        </repeat>

		<param name="attribute" type="text" size="40" value="protein" label="Attribute to use for filtering" help="Must be an attribute of a pepXML search_hit node. For example, protein or peptide">
	    	<sanitizer>
        	<valid initial="string.printable">
         	<remove value="&apos;"/>
        	</valid>
        	<mapping initial="none">
          	<add source="&apos;" target="__sq__"/>
        	</mapping>
      		</sanitizer>            	
        </param>

        <param name="reverse" type="boolean" label="Keep mismatches instead of matches" truevalue="--reject" falsevalue="" />

        <param name="check_alt" type="boolean" label="Check alternative_protein entries" truevalue="--check-alternatives" falsevalue="" help="Also apply the search filter to the protein attribute of alternative_protein entries under each search_hit. A match to any counts as a match."/>

	</inputs>

	<outputs>
		<data format="pepxml" name="output" />
	</outputs>


  <help>

**What it does**

Filters PSMs in a pepXML file keeping only those that match filtering criteria

----

**References**


  </help>

</tool>