Mercurial > repos > galaxyp > openms_psmfeatureextractor

comparison PSMFeatureExtractor.xml @ 0:16a3498124d1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:40:23 -0500
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children 54ff34feb43d
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-1:000000000000 0:16a3498124d1
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="2.3.0">
5 <description>Computes extra features for each input PSM.</description>
6 <macros>
7 <token name="@EXECUTABLE@">PSMFeatureExtractor</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>PSMFeatureExtractor
14
15 -in
16 #for token in $param_in:
17 $token
18 #end for
19 #if $param_out:
20 -out $param_out
21 #end if
22
23 #if $rep_param_extra:
24 -extra
25 #for token in $rep_param_extra:
26 #if " " in str(token):
27 "$token.param_extra"
28 #else
29 $token.param_extra
30 #end if
31 #end for
32 #end if
33 #if $param_multiple_search_engines:
34 -multiple_search_engines
35 #end if
36 #if $adv_opts.adv_opts_selector=='advanced':
37 #if $adv_opts.param_skip_db_check:
38 -skip_db_check
39 #end if
40 #if $adv_opts.param_concat:
41 -concat
42 #end if
43 #if $adv_opts.param_impute:
44 -impute
45 #end if
46 #if $adv_opts.param_limit_imputation:
47 -limit_imputation
48 #end if
49 #if $adv_opts.param_force:
50 -force
51 #end if
52 #end if
53 </command>
54 <inputs>
55 <param name="param_in" type="data" format="mzid,idxml" multiple="true" optional="False" size="30" label="Input file(s)" help="(-in) ">
56 <sanitizer>
57 <valid initial="string.printable">
58 <remove value="'"/>
59 <remove value="&quot;"/>
60 </valid>
61 </sanitizer>
62 </param>
63 <repeat name="rep_param_extra" min="0" title="param_extra">
64 <param name="param_extra" type="text" size="30" label="List of the MetaData parameters to be included in a feature set for precolato" help="(-extra) ">
65 <sanitizer>
66 <valid initial="string.printable">
67 <remove value="'"/>
68 <remove value="&quot;"/>
69 </valid>
70 </sanitizer>
71 </param>
72 </repeat>
73 <param name="param_multiple_search_engines" display="radio" type="boolean" truevalue="-multiple_search_engines" falsevalue="" checked="false" optional="True" label="Combine PSMs from different search engines by merging on scan level" help="(-multiple_search_engines) "/>
74 <expand macro="advanced_options">
75 <param name="param_skip_db_check" display="radio" type="boolean" truevalue="-skip_db_check" falsevalue="" checked="false" optional="True" label="Manual override to skip the check if same settings for multiple search engines were applied" help="(-skip_db_check) Only valid together with -multiple_search_engines flag"/>
76 <param name="param_concat" display="radio" type="boolean" truevalue="-concat" falsevalue="" checked="false" optional="True" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="(-concat) Only valid together with -multiple_search_engines flag"/>
77 <param name="param_impute" display="radio" type="boolean" truevalue="-impute" falsevalue="" checked="false" optional="True" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="(-impute) Only valid together with -multiple_search_engines flag"/>
78 <param name="param_limit_imputation" display="radio" type="boolean" truevalue="-limit_imputation" falsevalue="" checked="false" optional="True" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="(-limit_imputation) Only valid together with -multiple_search_engines flag"/>
79 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
80 </expand>
81 </inputs>
82 <outputs>
83 <data name="param_out" metadata_source="param_in" format="input"/>
84 </outputs>
85 <help>Computes extra features for each input PSM.
86
87
88 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_PSMFeatureExtractor.html</help>
89 </tool>