comparison FileMerger.xml @ 0:47d7f9fd5077 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:23:57 -0500
parents
children 1dc8550349dd
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-1:000000000000 0:47d7f9fd5077
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="&quot;"/>
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 &quot;file_origin&quot; (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 &gt; 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="&quot;"/>
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>