comparison delta_pi_calc.xml @ 1:8a30d6e5b97d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3

0:34c5c95740a1

<tool id="calc_delta_pi" name="Add delta pI" version="1.0">
    <requirements>
        <requirement type="package" version="3.6">python</requirement>
    </requirements>
    <description>to peptide table</description>
    <command>
	    python '$__tool_directory__/peptide_pi_annotator.py' -i '$trainingpi' -p '$peptable'
            --stripcol $stripcol --pepcol $pepcol --fraccol $fraccol --out '$output'
	    
	    --strippatterns
	    #for $strip in $strips
	        '$strip.pattern'
	    #end for

                      <remove preset="string.whitespace" /> 
		  </valid>
	      </sanitizer>
          </param>
      </repeat>
      <param name="pepcol" type="integer" value="" label="Peptide sequence column in peptide table" />
      <param name="fraccol" type="integer" value="" label="Fraction number column in peptide table" />
      <param name="stripcol" type="integer" value="" label="Strip pattern column in peptide table" help="E.g. column with filename to derive strip name from"/>
      <repeat name="strips" title="pI separation strip data">
	      <param name="pattern" type="text" label="Strip regex detection pattern" help="Regex (see help below) that identifies the pI strip from the column in the above field.">
                  <sanitizer>
                      <valid>
                          <remove preset="string.whitespace" />

                <param name="regex" value="*" />
            </repeat>
            <param name="pepcol" value="1" />
            <param name="fraccol" value="4" />
            <param name="stripcol" value="2" />
            <repeat name="strips">
                <param name="pattern" value="strip1" />
                <param name="intercept" value="8.21" />
                <param name="fr_width" value="0.013" />
            </repeat>

1:8a30d6e5b97d

<tool id="calc_delta_pi" name="Add delta pI" version="1.1">
    <requirements>
        <requirement type="package" version="3.6">python</requirement>
    </requirements>
    <description>to peptide table</description>
    <command>
	    python '$__tool_directory__/peptide_pi_annotator.py' -i '$trainingpi' -p '$peptable' --out '$output'
	    #if $stripcol
	        --stripcol $stripcol
	    #else if $stripcolpattern
	        --stripcolpattern '$stripcolpattern'
	    #end if
	    #if $pepcol
                --pepcol $pepcol 
	    #else if $pepcolpattern
                --pepcolpattern '$pepcolpattern'
	    #end if
	    #if $fraccol
                --fraccol $fraccol
	    #else if $fraccolpattern
                --fraccolpattern '$fraccolpattern'
	    #end if
	    
	    --strippatterns
	    #for $strip in $strips
	        '$strip.pattern'
	    #end for

                      <remove preset="string.whitespace" /> 
		  </valid>
	      </sanitizer>
          </param>
      </repeat>
      <param name="pepcolpattern" type="text" value="" optional="true" label="Peptide sequence pattern for column header field in peptide table." />
      <param name="pepcol" type="integer" value="" optional="true" label="Peptide sequence column number in peptide table. First column is 1. Overrides column pattern." />
      <param name="fraccolpattern" type="text" value="" optional="true" label="Fraction number column header papttern in peptide table." />
      <param name="fraccol" type="integer" optional="true" value="" label="Fraction number column number in peptide table. First column is 1. Overrides column pattern." />
      <param name="stripcolpattern" type="text" optional="true" value="" label="Strip pattern header column pattern in peptide table" help="E.g. column with filename to derive strip name from"/>
      <param name="stripcol" type="integer" optional="true" value="" label="Strip pattern column number in peptide table" help="E.g. column with filename to derive strip name from. First column is 1. Overrides column pattern"/>
      <repeat name="strips" title="pI separation strip data">
	      <param name="pattern" type="text" label="Strip regex detection pattern" help="Regex (see help below) that identifies the pI strip from the column in the above field.">
                  <sanitizer>
                      <valid>
                          <remove preset="string.whitespace" />

                <param name="regex" value="*" />
            </repeat>
            <param name="pepcol" value="1" />
            <param name="fraccol" value="4" />
            <param name="stripcol" value="2" />
            <repeat name="strips">
                <param name="pattern" value="strip1" />
                <param name="intercept" value="8.21" />
                <param name="fr_width" value="0.013" />
            </repeat>
            <repeat name="strips">
                <param name="pattern" value="strip2" />
                <param name="intercept" value="6.11" />
                <param name="fr_width" value="0.04" />
            </repeat>
            <output name="output" value="peptable_deltapi.txt" />
        </test>
        <test> 
            <param name="trainingpi" value="predicted_peptides.txt" />
            <param name="peptable" value="peptable.txt" />
            <repeat name="ignoremods">
                <param name="regex" value="*" />
            </repeat>
            <param name="pepcolpattern" value="Sequence" />
            <param name="fraccolpattern" value="Fraction" />
            <param name="stripcolpattern" value="Filename" />
            <repeat name="strips">
                <param name="pattern" value="strip1" />
                <param name="intercept" value="8.21" />
                <param name="fr_width" value="0.013" />
            </repeat>