Mercurial > repos > galaxyp > hirieftools
comparison pi_db_split.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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| -1:000000000000 | 0:34c5c95740a1 |
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| 1 <tool id="pi_db_split" name="Split peptide database" version="1.0"> | |
| 2 <description>into pI separated fractions</description> | |
| 3 <requirements> | |
| 4 <requirement type="package">numpy</requirement> | |
| 5 <requirement type="package" version="3.6">python</requirement> | |
| 6 </requirements> | |
| 7 <command> | |
| 8 <![CDATA[ | |
| 9 mkdir pi_fr_out && cd pi_fr_out && | |
| 10 python '$__tool_directory__/pi_database_splitter.py' -i '$pipeptides' -p '$peptable' | |
| 11 --intercept $intercept --width $fr_width --tolerance $tolerance --amount $fr_amount --prefix pisplit | |
| 12 --deltacol $deltacol --picutoff $picutoff | |
| 13 #if $fdrcol | |
| 14 --fdrcol $fdrcol --fdrcutoff $fdrcutoff | |
| 15 #end if | |
| 16 #if $reverse | |
| 17 --reverse | |
| 18 #end if | |
| 19 #if $maxlen | |
| 20 --maxlen $maxlen | |
| 21 #end if | |
| 22 --minlen $minlen | |
| 23 ]]> | |
| 24 </command> | |
| 25 | |
| 26 <inputs> | |
| 27 <param name="pipeptides" type="data" format="tabular" label="Target peptides with pI and accession" help="First col accession, second sequence, third pI" /> | |
| 28 <param name="peptable" type="data" format="tabular" label="Peptide table to determine pI shift from" help="Should have delta pI as a column" /> | |
| 29 <param name="fdrcol" type="integer" value="" optional="true" label="FDR (q-value) column in peptide table" /> | |
| 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" /> | |
| 31 <param name="deltacol" type="integer" value="" label="Delta pI column in peptide table" /> | |
| 32 <param name="picutoff" type="float" value="0.2" optional="true" label="delta-pI cutoff for inclusion in shift determination" /> | |
| 33 <param name="minlen" type="integer" value="8" label="Minimum length of peptide to include in split DB" /> | |
| 34 <param name="maxlen" type="integer" optional="true" value="" label="Max. length of peptide to include in split DB" /> | |
| 35 <param name="intercept" type="float" value="" label="Intercept of pI strip" /> | |
| 36 <param name="fr_width" type="float" value="" label="Fraction width" /> | |
| 37 <param name="tolerance" type="float" value="" label="pI tolerance" /> | |
| 38 <param name="fr_amount" type="integer" value="" label="Fraction amount" /> | |
| 39 <param name="reverse" type="boolean" label="Strip is reversed (high-to-low pI)?" /> | |
| 40 </inputs> | |
| 41 | |
| 42 <outputs> | |
| 43 <collection name="target_pi_db" type="list" label="target pI separated db"> | |
| 44 <discover_datasets pattern="pisplit_(?P<designation>.+)\.fasta" ext="fasta" directory="pi_fr_out" /> | |
| 45 </collection> | |
| 46 <collection name="decoy_pi_db" type="list" label="decoy pI separated db"> | |
| 47 <discover_datasets pattern="decoy_pisplit_(?P<designation>.+)\.fasta" ext="fasta" directory="pi_fr_out" /> | |
| 48 </collection> | |
| 49 </outputs> | |
| 50 <tests> | |
| 51 <test> | |
| 52 <param name="pipeptides" value="predicted_peptides_to_split.txt" /> | |
| 53 <param name="peptable" value="peptable_deltapi.txt" /> | |
| 54 <param name="fdrcol" value="3" /> | |
| 55 <param name="fdrcutoff" value="0.2" /> | |
| 56 <param name="deltacol" value="-1" /> | |
| 57 <param name="picutoff" value="10" /> | |
| 58 <param name="minlen" value="8" /> | |
| 59 <param name="intercept" value="5.6" /> | |
| 60 <param name="fr_width" value="1.3" /> | |
| 61 <param name="tolerance" value="0.1" /> | |
| 62 <param name="fr_amount" value="3" /> | |
| 63 <param name="reverse" value="false" /> | |
| 64 <output_collection name="target_pi_db" type="list"> | |
| 65 <element name="fr1" value="target_splitdb_fr1.fasta" /> | |
| 66 <element name="fr2" value="target_splitdb_fr2.fasta" /> | |
| 67 <element name="fr3" value="target_splitdb_fr3.fasta" /> | |
| 68 </output_collection> | |
| 69 <output_collection name="decoy_pi_db" type="list"> | |
| 70 <element name="fr1" value="decoy_splitdb_fr1.fasta" /> | |
| 71 <element name="fr2" value="decoy_splitdb_fr2.fasta" /> | |
| 72 <element name="fr3" value="decoy_splitdb_fr3.fasta" /> | |
| 73 </output_collection> | |
| 74 </test> | |
| 75 </tests> | |
| 76 | |
| 77 <help> | |
| 78 Creates a pI separated database collection from a pI-determined input | |
| 79 file of peptide/protein mappings. Outputs one db for target, one | |
| 80 for decoy. | |
| 81 </help> | |
| 82 | |
| 83 </tool> |