Mercurial > repos > galaxyp > openms_idscoreswitcher

comparison IDScoreSwitcher.xml @ 0:96484de4d4bd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:26:54 -0500
parents
children a0354cc9a256
comparison
equal deleted inserted replaced
-1:000000000000 0:96484de4d4bd
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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="2.1.0">
5 <description>Switches between different scores of peptide or protein hits in identification data</description>
6 <macros>
7 <token name="@EXECUTABLE@">IDScoreSwitcher</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>IDScoreSwitcher
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_new_score:
22 -new_score "$param_new_score"
23 #end if
24 #if $param_new_score_orientation:
25 -new_score_orientation
26 #if " " in str($param_new_score_orientation):
27 "$param_new_score_orientation"
28 #else
29 $param_new_score_orientation
30 #end if
31 #end if
32 #if $param_new_score_type:
33 -new_score_type "$param_new_score_type"
34 #end if
35 #if $param_old_score:
36 -old_score "$param_old_score"
37 #end if
38 #if $param_proteins:
39 -proteins
40 #end if
41 #if $adv_opts.adv_opts_selector=='advanced':
42 #if $adv_opts.param_force:
43 -force
44 #end if
45 #end if
46 </command>
47 <inputs>
48 <param name="param_in" type="data" format="idxml" optional="False" label="Input file" help="(-in) "/>
49 <param name="param_new_score" type="text" size="30" label="Name of the meta value to use as the new score" help="(-new_score) ">
50 <sanitizer>
51 <valid initial="string.printable">
52 <remove value="'"/>
53 <remove value="&quot;"/>
54 </valid>
55 </sanitizer>
56 </param>
57 <param name="param_new_score_orientation" display="radio" type="select" optional="False" label="Orientation of the new score (are higher or lower values better?)" help="(-new_score_orientation) ">
58 <option value="lower_better">lower_better</option>
59 <option value="higher_better">higher_better</option>
60 </param>
61 <param name="param_new_score_type" type="text" size="30" label="Name to use as the type of the new score (default: same as 'new_score')" help="(-new_score_type) ">
62 <sanitizer>
63 <valid initial="string.printable">
64 <remove value="'"/>
65 <remove value="&quot;"/>
66 </valid>
67 </sanitizer>
68 </param>
69 <param name="param_old_score" type="text" size="30" label="Name to use for the meta value storing the old score (default: old score type)" help="(-old_score) ">
70 <sanitizer>
71 <valid initial="string.printable">
72 <remove value="'"/>
73 <remove value="&quot;"/>
74 </valid>
75 </sanitizer>
76 </param>
77 <param name="param_proteins" display="radio" type="boolean" truevalue="-proteins" falsevalue="" checked="false" optional="True" label="Apply to protein scores instead of PSM scores" help="(-proteins) "/>
78 <expand macro="advanced_options">
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" format="idxml"/>
84 </outputs>
85 <help>Switches between different scores of peptide or protein hits in identification data
86
87
88 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDScoreSwitcher.html</help>
89 </tool>