Mercurial > repos > galaxyp > openms_filemerger

comparison FileMerger.xml @ 13:37ae36c2b22d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 06:48:49 -0400
parents 33e3f62dcf23
children 3d6d358dab7d
comparison
equal deleted inserted replaced
12:265ae579572f 13:37ae36c2b22d
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="FileMerger" name="FileMerger" version="2.2.0"> 4 <tool id="FileMerger" name="FileMerger" version="2.3.0">
5 <description>Merges several MS files into one file.</description> 5 <description>Merges several MS files into one file.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FileMerger</token> 7 <token name="@EXECUTABLE@">FileMerger</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>FileMerger 13 <command detect_errors="aggressive"><![CDATA[FileMerger
14 14
15 -in 15 -in
16 #for token in $param_in: 16 #for token in $param_in:
17 $token 17 $token
18 #end for 18 #end for
24 #end if 24 #end if
25 #if $param_rt_concat_gap: 25 #if $param_rt_concat_gap:
26 -rt_concat:gap $param_rt_concat_gap 26 -rt_concat:gap $param_rt_concat_gap
27 #end if 27 #end if
28 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
29 #if $param_raw_rt_auto: 39 #if $param_raw_rt_auto:
30 -raw:rt_auto 40 -raw:rt_auto
31 #end if 41 #end if
32 42
33 #if $rep_param_raw_rt_custom: 43 #if $rep_param_raw_rt_custom:
49 #if $adv_opts.adv_opts_selector=='advanced': 59 #if $adv_opts.adv_opts_selector=='advanced':
50 #if $adv_opts.param_force: 60 #if $adv_opts.param_force:
51 -force 61 -force
52 #end if 62 #end if
53 #end if 63 #end if
54 </command> 64 ]]></command>
55 <inputs> 65 <inputs>
56 <param name="param_in" type="data" format="mzData,mzxml,mzml,dta,dta2d,mgf,featurexml,consensusxml,fid,traml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) "> 66 <param name="param_in" type="data" format="mzData,mzxml,mzml,dta,dta2d,mgf,featurexml,consensusxml,fid,traml,fasta" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
57 <sanitizer> 67 <sanitizer>
58 <valid initial="string.printable"> 68 <valid initial="string.printable">
59 <remove value="'"/> 69 <remove value="'"/>
60 <remove value="&quot;"/> 70 <remove value="&quot;"/>
61 </valid> 71 </valid>
63 </param> 73 </param>
64 <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) "/> 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) "/>
65 <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"/> 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"/>
66 <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) "/> 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) "/>
67 <repeat name="rep_param_raw_rt_custom" min="0" title="param_raw_rt_custom"> 77 <repeat name="rep_param_raw_rt_custom" min="0" title="param_raw_rt_custom">
68 <param name="param_raw_rt_custom" type="text" size="30" value="0" label="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"> 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">
69 <sanitizer> 79 <sanitizer>
70 <valid initial="string.printable"> 80 <valid initial="string.printable">
71 <remove value="'"/> 81 <remove value="'"/>
72 <remove value="&quot;"/> 82 <remove value="&quot;"/>
73 </valid> 83 </valid>
79 <expand macro="advanced_options"> 89 <expand macro="advanced_options">
80 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
81 </expand> 91 </expand>
82 </inputs> 92 </inputs>
83 <outputs> 93 <outputs>
84 <data name="param_out" format="mzml"/> 94 <data name="param_out" format="featurexml"/>
95 <data name="param_rt_concat_trafo_out" format="trafoxml"/>
85 </outputs> 96 </outputs>
86 <help>Merges several MS files into one file. 97 <help>Merges several MS files into one file.
87 98
88 99
89 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html</help> 100 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FileMerger.html</help>
90 </tool> 101 </tool>