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annotate pi_db_split.xml @ 0:34c5c95740a1 draft

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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
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children 8a30d6e5b97d
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34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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1 <tool id="pi_db_split" name="Split peptide database" version="1.0">
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2 <description>into pI separated fractions</description>
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3 <requirements>
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4 <requirement type="package">numpy</requirement>
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5 <requirement type="package" version="3.6">python</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 mkdir pi_fr_out && cd pi_fr_out &&
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10 python '$__tool_directory__/pi_database_splitter.py' -i '$pipeptides' -p '$peptable'
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11 --intercept $intercept --width $fr_width --tolerance $tolerance --amount $fr_amount --prefix pisplit
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12 --deltacol $deltacol --picutoff $picutoff
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13 #if $fdrcol
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14 --fdrcol $fdrcol --fdrcutoff $fdrcutoff
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15 #end if
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16 #if $reverse
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17 --reverse
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18 #end if
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19 #if $maxlen
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20 --maxlen $maxlen
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21 #end if
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22 --minlen $minlen
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23 ]]>
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24 </command>
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25
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26 <inputs>
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27 <param name="pipeptides" type="data" format="tabular" label="Target peptides with pI and accession" help="First col accession, second sequence, third pI" />
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28 <param name="peptable" type="data" format="tabular" label="Peptide table to determine pI shift from" help="Should have delta pI as a column" />
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29 <param name="fdrcol" type="integer" value="" optional="true" label="FDR (q-value) column in peptide table" />
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30 <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" />
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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31 <param name="deltacol" type="integer" value="" label="Delta pI column in peptide table" />
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32 <param name="picutoff" type="float" value="0.2" optional="true" label="delta-pI cutoff for inclusion in shift determination" />
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33 <param name="minlen" type="integer" value="8" label="Minimum length of peptide to include in split DB" />
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34 <param name="maxlen" type="integer" optional="true" value="" label="Max. length of peptide to include in split DB" />
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35 <param name="intercept" type="float" value="" label="Intercept of pI strip" />
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36 <param name="fr_width" type="float" value="" label="Fraction width" />
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37 <param name="tolerance" type="float" value="" label="pI tolerance" />
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38 <param name="fr_amount" type="integer" value="" label="Fraction amount" />
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39 <param name="reverse" type="boolean" label="Strip is reversed (high-to-low pI)?" />
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40 </inputs>
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41
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42 <outputs>
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43 <collection name="target_pi_db" type="list" label="target pI separated db">
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44 <discover_datasets pattern="pisplit_(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="pi_fr_out" />
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45 </collection>
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46 <collection name="decoy_pi_db" type="list" label="decoy pI separated db">
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47 <discover_datasets pattern="decoy_pisplit_(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="pi_fr_out" />
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48 </collection>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="pipeptides" value="predicted_peptides_to_split.txt" />
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53 <param name="peptable" value="peptable_deltapi.txt" />
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54 <param name="fdrcol" value="3" />
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55 <param name="fdrcutoff" value="0.2" />
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56 <param name="deltacol" value="-1" />
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57 <param name="picutoff" value="10" />
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58 <param name="minlen" value="8" />
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59 <param name="intercept" value="5.6" />
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60 <param name="fr_width" value="1.3" />
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61 <param name="tolerance" value="0.1" />
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62 <param name="fr_amount" value="3" />
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63 <param name="reverse" value="false" />
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64 <output_collection name="target_pi_db" type="list">
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65 <element name="fr1" value="target_splitdb_fr1.fasta" />
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66 <element name="fr2" value="target_splitdb_fr2.fasta" />
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67 <element name="fr3" value="target_splitdb_fr3.fasta" />
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68 </output_collection>
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69 <output_collection name="decoy_pi_db" type="list">
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70 <element name="fr1" value="decoy_splitdb_fr1.fasta" />
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71 <element name="fr2" value="decoy_splitdb_fr2.fasta" />
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72 <element name="fr3" value="decoy_splitdb_fr3.fasta" />
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73 </output_collection>
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74 </test>
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75 </tests>
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76
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77 <help>
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78 Creates a pI separated database collection from a pI-determined input
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79 file of peptide/protein mappings. Outputs one db for target, one
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80 for decoy.
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81 </help>
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82
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83 </tool>