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comparison filter_psms.xml @ 3:86fd1757f102 draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98
author iracooke
date Mon, 21 Dec 2015 23:43:55 -0500
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2:68d8c9e521d7 3:86fd1757f102
1 <tool id="filter_psms" name="Filter PSMs" version="1.0.0">
2 <description>Select PSMs in a pepXML file matching criteria</description>
3
4 <requirements>
5 <requirement type="package" version="1.4">protk</requirement>
6 </requirements>
7
8 <command>
9 filter_psms.rb
10
11 '
12 $first_expression
13 #for $expression in $expressions:
14 ,${expression.expression}
15 #end for
16 '
17
18 $pepxml_file
19
20 --attribute $attribute
21
22 $check_alt
23
24 $reverse
25
26 -o $output
27
28
29 </command>
30
31 <stdio>
32 <exit_code range="1:" level="fatal" description="Failure" />
33 </stdio>
34
35 <inputs>
36
37 <param name="pepxml_file" type="data" format="pepxml,raw_pepxml" multiple="false" label="Proteomics Search Results" help="A pepXML file"/>
38
39
40 <param name="first_expression" type="text" size="40" value="decoy_" label="Expression">
41 <sanitizer>
42 <valid initial="string.printable">
43 <remove value="&apos;"/>
44 </valid>
45 <mapping initial="none">
46 <add source="&apos;" target="__sq__"/>
47 </mapping>
48 </sanitizer>
49 </param>
50
51 <repeat name="expressions" title="Expressions to Match against" help="These can include regular expressions">
52 <param name="expression" type="text" size="40" value="decoy_" label="Expression">
53 <sanitizer>
54 <valid initial="string.printable">
55 <remove value="&apos;"/>
56 </valid>
57 <mapping initial="none">
58 <add source="&apos;" target="__sq__"/>
59 </mapping>
60 </sanitizer>
61 </param>
62 </repeat>
63
64 <param name="attribute" type="text" size="40" value="protein" label="Attribute to use for filtering" help="Must be an attribute of a pepXML search_hit node. For example, protein or peptide">
65 <sanitizer>
66 <valid initial="string.printable">
67 <remove value="&apos;"/>
68 </valid>
69 <mapping initial="none">
70 <add source="&apos;" target="__sq__"/>
71 </mapping>
72 </sanitizer>
73 </param>
74
75 <param name="reverse" type="boolean" label="Keep mismatches instead of matches" truevalue="--reject" falsevalue="" />
76
77 <param name="check_alt" type="boolean" label="Check alternative_protein entries" truevalue="--check-alternatives" falsevalue="" help="Also apply the search filter to the protein attribute of alternative_protein entries under each search_hit. A match to any counts as a match."/>
78
79 </inputs>
80
81 <outputs>
82 <data format="pepxml" name="output" />
83 </outputs>
84
85
86 <help>
87
88 **What it does**
89
90 Filters PSMs in a pepXML file keeping only those that match filtering criteria
91
92 ----
93
94 **References**
95
96
97 </help>
98
99 </tool>