Mercurial > repos > galaxyp > hirieftools
diff delta_pi_calc.xml @ 0:34c5c95740a1 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
| author | galaxyp |
|---|---|
| date | Mon, 22 May 2017 05:08:23 -0400 |
| parents | |
| children | 8a30d6e5b97d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/delta_pi_calc.xml Mon May 22 05:08:23 2017 -0400 @@ -0,0 +1,146 @@ +<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 + + --intercepts + #for $strip in $strips + $strip.intercept + #end for + + --widths + #for $strip in $strips + $strip.fr_width + #end for + + #if len($ignoremods) > 0 + --ignoremods + #for $mod in $ignoremods + '$mod.regex' + #end for + #end if + </command> + + <inputs> + <param name="trainingpi" type="data" format="tabular" label="Known peptides with annotation of pI" help="First column is sequence, second pI" /> + <param name="peptable" type="data" format="tabular" label="Peptide table to determine pI shift from" /> + <repeat name="ignoremods" title="Peptide modification weights to ignore"> + <param name="regex" label="Regex to strip modification from peptide table before looking up sequence in predicted pI" type="text" help="Enter e.g. 15.994915 for oxidation, * to ignore all modifications, or a proper regex (however brackets are stripped by galaxy). See help below."> + <sanitizer> + <valid> + <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" /> + </valid> + </sanitizer> + </param> + <param name="intercept" type="text" label="pI intercept of strip" /> + <param name="fr_width" type="text" label="fraction widths" /> + </repeat> + </inputs> + + <outputs> + <data format="tabular" name="output"/> + </outputs> + <tests> + <test> + <param name="trainingpi" value="predicted_peptides.txt" /> + <param name="peptable" value="peptable.txt" /> + <repeat name="ignoremods"> + <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="15.994915" /> + </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" /> + <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_missed_ox.txt" /> + </test> + </tests> + + <help> + In case you have no pI calculation method but a large table with + peptides and their predicted pIs available. This tool adds a column + with delta-pI values to a peptide or PSM table for each peptide it + can find in the predicted collection. Needs a tab-separated file + with peptide-sequences and their predicted pI, and a PSM/peptide table + with at least peptide sequences. + + Regexes, or regular expressions are are sequences of characters that + are used to find a certain pattern in a string of text. For example + the regex "peptide" will find the word "peptide" in the text + "thisisa peptide in my sample". More advanced regexes can allow for + finding for example specific but variable pieces of text, e.g. + "[a-c].*" will match a string "acbcba" in "yxyzyxacbcbayxzyxyzxy". + Much more elaborate regexes exist. Since this is a python script, + python regexes are described here: + https://docs.python.org/3/library/re.html + </help> + +</tool>