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