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comparison FileMerger.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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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="&quot;"/>
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 &quot;file_origin&quot; (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="&quot;"/>
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) &lt;br&gt;This option is useful for merging DTA file, which should contain the string &lt;br&gt;'rt' directly followed by a floating point number: &lt;br&gt;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>