view pi_db_split.xml @ 0:34c5c95740a1 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d

<tool id="pi_db_split" name="Split peptide database" version="1.0">
    <description>into pI separated fractions</description>
    <requirements>
        <requirement type="package">numpy</requirement>
        <requirement type="package" version="3.6">python</requirement>
    </requirements>
    <command>
	    <![CDATA[
	    mkdir pi_fr_out && cd pi_fr_out &&
	    python '$__tool_directory__/pi_database_splitter.py' -i '$pipeptides' -p '$peptable'
            --intercept $intercept --width $fr_width --tolerance $tolerance --amount $fr_amount --prefix pisplit
	    --deltacol $deltacol --picutoff $picutoff 
	    #if $fdrcol
	        --fdrcol $fdrcol --fdrcutoff $fdrcutoff 
	    #end if
            #if $reverse
                --reverse
            #end if
            #if $maxlen
                --maxlen $maxlen
            #end if
            --minlen $minlen
	    ]]>
    </command>
    
    <inputs>
      <param name="pipeptides" type="data" format="tabular" label="Target peptides with pI and accession" help="First col accession, second sequence, third pI" />
      <param name="peptable" type="data" format="tabular" label="Peptide table to determine pI shift from" help="Should have delta pI as a column" />
      <param name="fdrcol" type="integer" value="" optional="true" label="FDR (q-value) column in peptide table" />
      <param name="fdrcutoff" type="float" value="0.0" help="Not used when no FDR column specified" label="FDR value cutoff for inclusion in shift determination" />
      <param name="deltacol" type="integer" value="" label="Delta pI column in peptide table" />
      <param name="picutoff" type="float" value="0.2" optional="true" label="delta-pI cutoff for inclusion in shift determination" />
      <param name="minlen" type="integer" value="8" label="Minimum length of peptide to include in split DB" />
      <param name="maxlen" type="integer" optional="true" value="" label="Max. length of peptide to include in split DB" />
      <param name="intercept" type="float" value="" label="Intercept of pI strip" />
      <param name="fr_width" type="float" value="" label="Fraction width" />
      <param name="tolerance" type="float" value="" label="pI tolerance" />
      <param name="fr_amount" type="integer" value="" label="Fraction amount" />
      <param name="reverse" type="boolean" label="Strip is reversed (high-to-low pI)?" />
    </inputs>
    
    <outputs>
	<collection name="target_pi_db" type="list" label="target pI separated db">
            <discover_datasets pattern="pisplit_(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="pi_fr_out" />
	</collection>
	<collection name="decoy_pi_db" type="list" label="decoy pI separated db">
            <discover_datasets pattern="decoy_pisplit_(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="pi_fr_out" />
	</collection>
    </outputs>
    <tests>
	    <test>
		    <param name="pipeptides" value="predicted_peptides_to_split.txt" />
		    <param name="peptable" value="peptable_deltapi.txt" />
		    <param name="fdrcol" value="3" />
		    <param name="fdrcutoff" value="0.2" />
		    <param name="deltacol" value="-1" />
		    <param name="picutoff" value="10" />
		    <param name="minlen" value="8" />
		    <param name="intercept" value="5.6" />
		    <param name="fr_width" value="1.3" />
		    <param name="tolerance" value="0.1" />
		    <param name="fr_amount" value="3" />
		    <param name="reverse" value="false" />
		    <output_collection name="target_pi_db" type="list">
			    <element name="fr1" value="target_splitdb_fr1.fasta" />
			    <element name="fr2" value="target_splitdb_fr2.fasta" />
			    <element name="fr3" value="target_splitdb_fr3.fasta" />
		    </output_collection>
		    <output_collection name="decoy_pi_db" type="list">
			    <element name="fr1" value="decoy_splitdb_fr1.fasta" />
			    <element name="fr2" value="decoy_splitdb_fr2.fasta" />
			    <element name="fr3" value="decoy_splitdb_fr3.fasta" />
		    </output_collection>
	    </test>
    </tests>

    <help>
	    Creates a pI separated database collection from a pI-determined input
	    file of peptide/protein mappings. Outputs one db for target, one
	    for decoy.
    </help>

</tool>