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comparison pi_db_split.xml @ 1:8a30d6e5b97d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3
author galaxyp
date Mon, 24 Jul 2017 05:25:22 -0400
parents 34c5c95740a1
children 77ddaee887a8
comparison
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0:34c5c95740a1 1:8a30d6e5b97d
1 <tool id="pi_db_split" name="Split peptide database" version="1.0"> 1 <tool id="pi_db_split" name="Split peptide database" version="1.1">
2 <description>into pI separated fractions</description> 2 <description>into pI separated fractions</description>
3 <requirements> 3 <requirements>
4 <requirement type="package">numpy</requirement> 4 <requirement type="package">numpy</requirement>
5 <requirement type="package" version="3.6">python</requirement> 5 <requirement type="package" version="3.6">python</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 <![CDATA[ 8 <![CDATA[
9 mkdir pi_fr_out && cd pi_fr_out && 9 mkdir pi_fr_out && cd pi_fr_out &&
10 python '$__tool_directory__/pi_database_splitter.py' -i '$pipeptides' -p '$peptable' 10 python '$__tool_directory__/pi_database_splitter.py' -i '$pipeptides' -p '$peptable'
11 --intercept $intercept --width $fr_width --tolerance $tolerance --amount $fr_amount --prefix pisplit 11 #for $strip in $strips
12 --deltacol $deltacol --picutoff $picutoff 12 #if not $strip.peptable_pattern or str($strip.peptable_pattern) in $peptable.element_identifier
13 --intercept $strip.intercept --width $strip.fr_width --tolerance $strip.tolerance --amount $strip.fr_amount --prefix pisplit --picutoff $strip.picutoff
14 #if $strip.reverse
15 --reverse
16 #end if
17 #break
18 #end if
19 #end for
20
21 #if $deltacol
22 --deltacol $deltacol
23 #else if $deltacolpattern
24 --deltacolpattern '$deltacolpattern'
25 #end if
13 #if $fdrcol 26 #if $fdrcol
14 --fdrcol $fdrcol --fdrcutoff $fdrcutoff 27 --fdrcol $fdrcol --fdrcutoff $fdrcutoff
28 #else if $fdrcolpattern
29 --fdrcolpattern '$fdrcolpattern' --fdrcutoff $fdrcutoff
15 #end if 30 #end if
16 #if $reverse
17 --reverse
18 #end if
19 #if $maxlen 31 #if $maxlen
20 --maxlen $maxlen 32 --maxlen $maxlen
21 #end if 33 #end if
22 --minlen $minlen 34 --minlen $minlen
23 ]]> 35 ]]>
24 </command> 36 </command>
25 37
26 <inputs> 38 <inputs>
27 <param name="pipeptides" type="data" format="tabular" label="Target peptides with pI and accession" help="First col accession, second sequence, third pI" /> 39 <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" /> 40 <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" /> 41 <param name="fdrcolpattern" type="text" optional="true" label="FDR (q-value) column pattern in peptide table" />
42 <param name="fdrcol" type="integer" value="" optional="true" label="FDR (q-value) column number in peptide table" help="Overrides column pattern if filled. First column is 1" />
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" /> 43 <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" /> 44 <param name="deltacolpattern" type="text" value="" label="Delta pI column pattern in peptide table" />
32 <param name="picutoff" type="float" value="0.2" optional="true" label="delta-pI cutoff for inclusion in shift determination" /> 45 <param name="deltacol" type="integer" optional="true" value="" label="Delta pI column number in peptide table" help="Overrides column pattern if filled. First column is 1"/>
33 <param name="minlen" type="integer" value="8" label="Minimum length of peptide to include in split DB" /> 46 <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" /> 47 <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" /> 48 <repeat name="strips" title="pI separation strip data">
36 <param name="fr_width" type="float" value="" label="Fraction width" /> 49 <param name="peptable_pattern" type="text" label="Pattern to find correct peptide table for a strip, for when multiple peptide tables have different strips" help="Will match against peptide table's name. Leave blank for single peptide table or when using same strip in all tables" />
37 <param name="tolerance" type="float" value="" label="pI tolerance" /> 50 <param name="intercept" type="float" value="" label="Intercept of pI strip" />
38 <param name="fr_amount" type="integer" value="" label="Fraction amount" /> 51 <param name="fr_width" type="float" value="" label="Fraction width" />
39 <param name="reverse" type="boolean" label="Strip is reversed (high-to-low pI)?" /> 52 <param name="tolerance" type="float" value="" label="pI tolerance" />
53 <param name="fr_amount" type="integer" value="" label="Fraction amount" />
54 <param name="reverse" type="boolean" label="Strip is reversed (high-to-low pI)?" />
55 <param name="picutoff" type="float" value="0.2" optional="true" label="delta-pI cutoff for inclusion in shift determination" />
56 </repeat>
40 </inputs> 57 </inputs>
41 58
42 <outputs> 59 <outputs>
43 <collection name="target_pi_db" type="list" label="target pI separated db"> 60 <collection name="target_pi_db" type="list" label="target pI separated db">
44 <discover_datasets pattern="pisplit_(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="pi_fr_out" /> 61 <discover_datasets pattern="pisplit_(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="pi_fr_out" />
52 <param name="pipeptides" value="predicted_peptides_to_split.txt" /> 69 <param name="pipeptides" value="predicted_peptides_to_split.txt" />
53 <param name="peptable" value="peptable_deltapi.txt" /> 70 <param name="peptable" value="peptable_deltapi.txt" />
54 <param name="fdrcol" value="3" /> 71 <param name="fdrcol" value="3" />
55 <param name="fdrcutoff" value="0.2" /> 72 <param name="fdrcutoff" value="0.2" />
56 <param name="deltacol" value="-1" /> 73 <param name="deltacol" value="-1" />
57 <param name="picutoff" value="10" />
58 <param name="minlen" value="8" /> 74 <param name="minlen" value="8" />
59 <param name="intercept" value="5.6" /> 75 <repeat name="strips">
60 <param name="fr_width" value="1.3" /> 76 <param name="peptable_pattern" value="deltapi" />
61 <param name="tolerance" value="0.1" /> 77 <param name="intercept" value="5.6" />
62 <param name="fr_amount" value="3" /> 78 <param name="fr_width" value="1.3" />
63 <param name="reverse" value="false" /> 79 <param name="tolerance" value="0.1" />
80 <param name="fr_amount" value="3" />
81 <param name="reverse" value="false" />
82 <param name="picutoff" value="10" />
83 </repeat>
84 <output_collection name="target_pi_db" type="list">
85 <element name="fr1" value="target_splitdb_fr1.fasta" />
86 <element name="fr2" value="target_splitdb_fr2.fasta" />
87 <element name="fr3" value="target_splitdb_fr3.fasta" />
88 </output_collection>
89 <output_collection name="decoy_pi_db" type="list">
90 <element name="fr1" value="decoy_splitdb_fr1.fasta" />
91 <element name="fr2" value="decoy_splitdb_fr2.fasta" />
92 <element name="fr3" value="decoy_splitdb_fr3.fasta" />
93 </output_collection>
94 </test>
95 <test>
96 <param name="pipeptides" value="predicted_peptides_to_split.txt" />
97 <param name="peptable" value="peptable_deltapi.txt" />
98 <param name="fdrcolpattern" value="FDR" />
99 <param name="fdrcutoff" value="0.2" />
100 <param name="deltacolpattern" value="Delta" />
101 <param name="minlen" value="8" />
102 <repeat name="strips">
103 <param name="intercept" value="5.6" />
104 <param name="fr_width" value="1.3" />
105 <param name="tolerance" value="0.1" />
106 <param name="fr_amount" value="3" />
107 <param name="reverse" value="false" />
108 <param name="picutoff" value="10" />
109 </repeat>
64 <output_collection name="target_pi_db" type="list"> 110 <output_collection name="target_pi_db" type="list">
65 <element name="fr1" value="target_splitdb_fr1.fasta" /> 111 <element name="fr1" value="target_splitdb_fr1.fasta" />
66 <element name="fr2" value="target_splitdb_fr2.fasta" /> 112 <element name="fr2" value="target_splitdb_fr2.fasta" />
67 <element name="fr3" value="target_splitdb_fr3.fasta" /> 113 <element name="fr3" value="target_splitdb_fr3.fasta" />
68 </output_collection> 114 </output_collection>