|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="FileMerger" name="FileMerger" version="2.0.0">
|
|
|
3 <description>Merges several MS files into one file.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">FileMerger</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>FileMerger
|
|
|
11
|
|
|
12 -in
|
|
|
13 #for token in $param_in:
|
|
|
14 $token
|
|
|
15 #end for
|
|
|
16 #if $param_out:
|
|
|
17 -out $param_out
|
|
|
18 #end if
|
|
|
19 #if $param_annotate_file_origin:
|
|
|
20 -annotate_file_origin
|
|
|
21 #end if
|
|
|
22 -threads \${GALAXY_SLOTS:-24}
|
|
|
23 #if $param_raw_rt_auto:
|
|
|
24 -raw:rt_auto
|
|
|
25 #end if
|
|
|
26
|
|
|
27 #if $rep_param_raw_rt_custom:
|
|
|
28 -raw:rt_custom
|
|
|
29 #for token in $rep_param_raw_rt_custom:
|
|
|
30 #if " " in str(token):
|
|
|
31 "$token.param_raw_rt_custom"
|
|
|
32 #else
|
|
|
33 $token.param_raw_rt_custom
|
|
|
34 #end if
|
|
|
35 #end for
|
|
|
36 #end if
|
|
|
37 #if $param_raw_rt_filename:
|
|
|
38 -raw:rt_filename
|
|
|
39 #end if
|
|
|
40 #if $param_raw_ms_level:
|
|
|
41 -raw:ms_level $param_raw_ms_level
|
|
|
42 #end if
|
|
|
43 #if $param_raw_user_ms_level:
|
|
|
44 -raw:user_ms_level
|
|
|
45 #end if
|
|
|
46 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
47 #if $adv_opts.param_force:
|
|
|
48 -force
|
|
|
49 #end if
|
|
|
50 #end if
|
|
|
51 </command>
|
|
|
52 <inputs>
|
|
|
53 <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) ">
|
|
|
54 <sanitizer>
|
|
|
55 <valid initial="string.printable">
|
|
|
56 <remove value="'"/>
|
|
|
57 <remove value="""/>
|
|
|
58 </valid>
|
|
|
59 </sanitizer>
|
|
|
60 </param>
|
|
|
61 <param name="param_annotate_file_origin" 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) "/>
|
|
|
62 <param name="param_raw_rt_auto" type="boolean" truevalue="-raw:rt_auto" falsevalue="" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto) "/>
|
|
|
63 <repeat name="rep_param_raw_rt_custom" min="0" title="param_raw_rt_custom">
|
|
|
64 <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 given input file">
|
|
|
65 <sanitizer>
|
|
|
66 <valid initial="string.printable">
|
|
|
67 <remove value="'"/>
|
|
|
68 <remove value="""/>
|
|
|
69 </valid>
|
|
|
70 </sanitizer>
|
|
|
71 </param>
|
|
|
72 </repeat>
|
|
|
73 <param name="param_raw_rt_filename" type="boolean" truevalue="-raw:rt_filename" falsevalue="" checked="false" optional="True" label="If this flag is set FileMerger tries to guess the rt of the file name" help="(-rt_filename) <br>This option is useful for merging DTA file, which should contain the string <br>'rt' directly followed by a floating point number: <br>i.e. my_spectrum_rt2795.15.dta"/>
|
|
|
74 <param name="param_raw_ms_level" type="integer" value="2" label="This option is useful for use with DTA files which does not contain MS level information" help="(-ms_level) The given level is assigned to the spectra"/>
|
|
|
75 <param name="param_raw_user_ms_level" type="boolean" truevalue="-raw:user_ms_level" falsevalue="" checked="false" optional="True" label="If this flag is set, the MS level given above is used" help="(-user_ms_level) "/>
|
|
|
76 <expand macro="advanced_options">
|
|
|
77 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
78 </expand>
|
|
|
79 </inputs>
|
|
|
80 <outputs>
|
|
|
81 <data name="param_out" format="featurexml"/>
|
|
|
82 </outputs>
|
|
|
83 <help>**What it does**
|
|
|
84
|
|
|
85 Merges several MS files into one file.
|
|
|
86
|
|
|
87
|
|
|
88 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html</help>
|
|
|
89 <expand macro="references"/>
|
|
|
90 </tool>
|
