Mercurial > repos > galaxyp > openms_filemerger
comparison FileMerger.xml @ 0:47d7f9fd5077 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
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date | Wed, 01 Mar 2017 12:23:57 -0500 |
parents | |
children | 1dc8550349dd |
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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: [File Handling]--> | |
4 <tool id="FileMerger" name="FileMerger" version="2.1.0"> | |
5 <description>Merges several MS files into one file.</description> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">FileMerger</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="references"/> | |
11 <expand macro="stdio"/> | |
12 <expand macro="requirements"/> | |
13 <command>FileMerger | |
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 #if $param_annotate_file_origin: | |
23 -annotate_file_origin | |
24 #end if | |
25 #if $param_rt_concat_gap: | |
26 -rt_concat:gap $param_rt_concat_gap | |
27 #end if | |
28 | |
29 #if $rep_param_rt_concat_trafo_out: | |
30 -rt_concat:trafo_out | |
31 #for token in $rep_param_rt_concat_trafo_out: | |
32 #if " " in str(token): | |
33 "$token.param_rt_concat_trafo_out" | |
34 #else | |
35 $token.param_rt_concat_trafo_out | |
36 #end if | |
37 #end for | |
38 #end if | |
39 #if $param_raw_rt_auto: | |
40 -raw:rt_auto | |
41 #end if | |
42 | |
43 #if $rep_param_raw_rt_custom: | |
44 -raw:rt_custom | |
45 #for token in $rep_param_raw_rt_custom: | |
46 #if " " in str(token): | |
47 "$token.param_raw_rt_custom" | |
48 #else | |
49 $token.param_raw_rt_custom | |
50 #end if | |
51 #end for | |
52 #end if | |
53 #if $param_raw_rt_filename: | |
54 -raw:rt_filename | |
55 #end if | |
56 #if $param_raw_ms_level: | |
57 -raw:ms_level $param_raw_ms_level | |
58 #end if | |
59 #if $adv_opts.adv_opts_selector=='advanced': | |
60 #if $adv_opts.param_force: | |
61 -force | |
62 #end if | |
63 #end if | |
64 </command> | |
65 <inputs> | |
66 <param name="param_in" type="data" format="mgf,mzml,mzxml,traml,featurexml,consensusxml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) "> | |
67 <sanitizer> | |
68 <valid initial="string.printable"> | |
69 <remove value="'"/> | |
70 <remove value="""/> | |
71 </valid> | |
72 </sanitizer> | |
73 </param> | |
74 <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each feature using meta value "file_origin" (for featureXML and consensusXML only)" help="(-annotate_file_origin) "/> | |
75 <param name="param_rt_concat_gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="(-gap) RT concatenation is enabled if a value > 0 is set"/> | |
76 <param name="param_raw_rt_auto" display="radio" type="boolean" truevalue="-raw:rt_auto" falsevalue="" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto) "/> | |
77 <repeat name="rep_param_raw_rt_custom" min="0" max="1" title="param_raw_rt_custom"> | |
78 <param name="param_raw_rt_custom" type="text" size="30" value="0" label="List of custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files"> | |
79 <sanitizer> | |
80 <valid initial="string.printable"> | |
81 <remove value="'"/> | |
82 <remove value="""/> | |
83 </valid> | |
84 </sanitizer> | |
85 </param> | |
86 </repeat> | |
87 <param name="param_raw_rt_filename" display="radio" type="boolean" truevalue="-raw:rt_filename" falsevalue="" checked="false" optional="True" label="Try to guess the retention time of a file based on the filename. This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number," help="(-rt_filename) e.g. 'my_spectrum_rt2795.15.dta'"/> | |
88 <param name="param_raw_ms_level" type="integer" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="(-ms_level) This option is useful for DTA files which do not contain MS level information"/> | |
89 <expand macro="advanced_options"> | |
90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
91 </expand> | |
92 </inputs> | |
93 <outputs> | |
94 <data name="param_out" format="featurexml"/> | |
95 <data name="param_rt_concat_trafo_out" format="trafoxml"/> | |
96 </outputs> | |
97 <help>Merges several MS files into one file. | |
98 | |
99 | |
100 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html</help> | |
101 </tool> |