Mercurial > repos > galaxyp > hirieftools
annotate 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 |
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date | Mon, 22 May 2017 05:08:23 -0400 |
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children | 8a30d6e5b97d |
rev | line source |
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0
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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changeset
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1 <tool id="calc_delta_pi" name="Add delta pI" version="1.0"> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
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changeset
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2 <requirements> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
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3 <requirement type="package" version="3.6">python</requirement> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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changeset
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4 </requirements> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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5 <description>to peptide table</description> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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6 <command> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
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7 python '$__tool_directory__/peptide_pi_annotator.py' -i '$trainingpi' -p '$peptable' |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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8 --stripcol $stripcol --pepcol $pepcol --fraccol $fraccol --out '$output' |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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9 |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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10 --strippatterns |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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11 #for $strip in $strips |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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12 '$strip.pattern' |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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13 #end for |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
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14 |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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15 --intercepts |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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changeset
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16 #for $strip in $strips |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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17 $strip.intercept |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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18 #end for |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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19 |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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changeset
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20 --widths |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
diff
changeset
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21 #for $strip in $strips |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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22 $strip.fr_width |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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changeset
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23 #end for |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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24 |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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changeset
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25 #if len($ignoremods) > 0 |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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changeset
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26 --ignoremods |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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changeset
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27 #for $mod in $ignoremods |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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28 '$mod.regex' |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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29 #end for |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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30 #end if |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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31 </command> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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32 |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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changeset
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33 <inputs> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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changeset
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34 <param name="trainingpi" type="data" format="tabular" label="Known peptides with annotation of pI" help="First column is sequence, second pI" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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changeset
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35 <param name="peptable" type="data" format="tabular" label="Peptide table to determine pI shift from" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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36 <repeat name="ignoremods" title="Peptide modification weights to ignore"> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
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37 <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."> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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changeset
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38 <sanitizer> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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39 <valid> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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40 <remove preset="string.whitespace" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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41 </valid> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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42 </sanitizer> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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43 </param> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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44 </repeat> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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45 <param name="pepcol" type="integer" value="" label="Peptide sequence column in peptide table" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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46 <param name="fraccol" type="integer" value="" label="Fraction number column in peptide table" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
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47 <param name="stripcol" type="integer" value="" label="Strip pattern column in peptide table" help="E.g. column with filename to derive strip name from"/> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
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48 <repeat name="strips" title="pI separation strip data"> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
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49 <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."> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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50 <sanitizer> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
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51 <valid> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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52 <remove preset="string.whitespace" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
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53 </valid> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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parents:
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54 </sanitizer> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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parents:
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55 </param> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
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56 <param name="intercept" type="text" label="pI intercept of strip" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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57 <param name="fr_width" type="text" label="fraction widths" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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58 </repeat> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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59 </inputs> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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60 |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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61 <outputs> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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62 <data format="tabular" name="output"/> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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63 </outputs> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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64 <tests> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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65 <test> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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66 <param name="trainingpi" value="predicted_peptides.txt" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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67 <param name="peptable" value="peptable.txt" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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parents:
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68 <repeat name="ignoremods"> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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69 <param name="regex" value="*" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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70 </repeat> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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parents:
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71 <param name="pepcol" value="1" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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parents:
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72 <param name="fraccol" value="4" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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73 <param name="stripcol" value="2" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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74 <repeat name="strips"> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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75 <param name="pattern" value="strip1" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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76 <param name="intercept" value="8.21" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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77 <param name="fr_width" value="0.013" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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78 </repeat> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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79 <repeat name="strips"> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
parents:
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80 <param name="pattern" value="strip2" /> |
34c5c95740a1
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81 <param name="intercept" value="6.11" /> |
34c5c95740a1
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82 <param name="fr_width" value="0.04" /> |
34c5c95740a1
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83 </repeat> |
34c5c95740a1
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84 <output name="output" value="peptable_deltapi.txt" /> |
34c5c95740a1
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85 </test> |
34c5c95740a1
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86 <test> |
34c5c95740a1
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87 <param name="trainingpi" value="predicted_peptides.txt" /> |
34c5c95740a1
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88 <param name="peptable" value="peptable.txt" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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89 <repeat name="ignoremods"> |
34c5c95740a1
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90 <param name="regex" value="15.994915" /> |
34c5c95740a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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91 </repeat> |
34c5c95740a1
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92 <param name="pepcol" value="1" /> |
34c5c95740a1
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93 <param name="fraccol" value="4" /> |
34c5c95740a1
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94 <param name="stripcol" value="2" /> |
34c5c95740a1
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95 <repeat name="strips"> |
34c5c95740a1
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96 <param name="pattern" value="strip1" /> |
34c5c95740a1
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97 <param name="intercept" value="8.21" /> |
34c5c95740a1
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98 <param name="fr_width" value="0.013" /> |
34c5c95740a1
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99 </repeat> |
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100 <repeat name="strips"> |
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101 <param name="pattern" value="strip2" /> |
34c5c95740a1
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102 <param name="intercept" value="6.11" /> |
34c5c95740a1
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103 <param name="fr_width" value="0.04" /> |
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104 </repeat> |
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105 <output name="output" value="peptable_deltapi.txt" /> |
34c5c95740a1
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106 </test> |
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107 <test> |
34c5c95740a1
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108 <param name="trainingpi" value="predicted_peptides.txt" /> |
34c5c95740a1
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109 <param name="peptable" value="peptable.txt" /> |
34c5c95740a1
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110 <param name="pepcol" value="1" /> |
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111 <param name="fraccol" value="4" /> |
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112 <param name="stripcol" value="2" /> |
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113 <repeat name="strips"> |
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114 <param name="pattern" value="strip1" /> |
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115 <param name="intercept" value="8.21" /> |
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116 <param name="fr_width" value="0.013" /> |
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117 </repeat> |
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118 <repeat name="strips"> |
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119 <param name="pattern" value="strip2" /> |
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120 <param name="intercept" value="6.11" /> |
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121 <param name="fr_width" value="0.04" /> |
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122 </repeat> |
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123 <output name="output" value="peptable_missed_ox.txt" /> |
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124 </test> |
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125 </tests> |
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126 |
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127 <help> |
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128 In case you have no pI calculation method but a large table with |
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129 peptides and their predicted pIs available. This tool adds a column |
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130 with delta-pI values to a peptide or PSM table for each peptide it |
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131 can find in the predicted collection. Needs a tab-separated file |
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132 with peptide-sequences and their predicted pI, and a PSM/peptide table |
34c5c95740a1
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133 with at least peptide sequences. |
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134 |
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135 Regexes, or regular expressions are are sequences of characters that |
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136 are used to find a certain pattern in a string of text. For example |
34c5c95740a1
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137 the regex "peptide" will find the word "peptide" in the text |
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138 "thisisa peptide in my sample". More advanced regexes can allow for |
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139 finding for example specific but variable pieces of text, e.g. |
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140 "[a-c].*" will match a string "acbcba" in "yxyzyxacbcbayxzyxyzxy". |
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141 Much more elaborate regexes exist. Since this is a python script, |
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142 python regexes are described here: |
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143 https://docs.python.org/3/library/re.html |
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144 </help> |
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145 |
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146 </tool> |