annotate mzid_to_protxml.xml @ 2:68d8c9e521d7 draft

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

<tool id="mzid_to_protxml" name="mzIdentML to protXML" version="1.0.1">
	<description>Convert mzIdentML to protXML</description>

	<requirements>
		<container type="docker">iracooke/protk-1.4.3</container>		
		<requirement type="package" version="1.4.3">protk</requirement>
		<requirement type="package" version="2.2.29">blast+</requirement>
   </requirements>

	<command>
		mzid_to_protxml.rb $mzid_file 
				
		-o $output
	</command>

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

	<inputs>
		
		<param name="mzid_file" type="data" format="mzid" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/>

	</inputs>

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


	<tests>
	  <test>
	      <param name="mzid_file" value="PeptideShaker_tiny.mzid" format="mzid"/>
	      <output name="output" format="protxml">
	          <assert_contents>
	              <has_text text="JEMP01000061" />
	          </assert_contents>
	      </output>
	  </test>
	</tests>

  <help>

**What it does**

Roughly converts mzIdentML to protXML.  

At the present time, the conversion is really only designed to work with mzIdentML files produced by PeptideShaker and to produce protXML files suitable for input to protk proteogenomics tools. 


  </help>

</tool>