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comparison FileMerger.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="FileMerger" name="FileMerger" version="1.12.0"> 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 <description>Merges several MS files into one file.</description> 3 <!--Proposed Tool Section: [File Handling]-->
4 <macros> 4 <tool id="FileMerger" name="FileMerger" version="2.0.0">
5 <token name="@EXECUTABLE@">FileMerger</token> 5 <description>Merges several MS files into one file.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">FileMerger</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>FileMerger 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FileMerger
11 14
12 -in ${param_in} 15 -in
13 -in_type ${param_in_type} 16 #for token in $param_in:
14 -out ${param_out} 17 $token
15 ${param_annotate_file_origin} 18 #end for
16 -threads \${GALAXY_SLOTS:-24} 19 #if $param_out:
17 ${param_rt_auto} 20 -out $param_out
18 -raw:rt_custom ${param_rt_custom} 21 #end if
19 ${param_rt_filename} 22 #if $param_annotate_file_origin:
20 -raw:ms_level ${param_ms_level} 23 -annotate_file_origin
21 ${param_user_ms_level} 24 #end if
25 -threads \${GALAXY_SLOTS:-24}
26 #if $param_rt_concat_gap:
27 -rt_concat:gap $param_rt_concat_gap
28 #end if
29
30 ##if $rep_param_rt_concat_trafo_out:
31 ##-rt_concat:trafo_out
32 ## #for token in $rep_param_rt_concat_trafo_out:
33 ## #if &quot; &quot; in str(token):
34 ## &quot;$token.param_rt_concat_trafo_out&quot;
35 ## #else
36 ## $token.param_rt_concat_trafo_out
37 ## #end if
38 ## #end for
39 ###end if
40
41 #if $param_raw_rt_auto:
42 -raw:rt_auto
43 #end if
44
45 #if $rep_param_raw_rt_custom:
46 -raw:rt_custom
47 #for token in $rep_param_raw_rt_custom:
48 #if &quot; &quot; in str(token):
49 &quot;$token.param_raw_rt_custom&quot;
50 #else
51 $token.param_raw_rt_custom
52 #end if
53 #end for
54 #end if
55 #if $param_raw_rt_filename:
56 -raw:rt_filename
57 #end if
58 #if $param_raw_ms_level:
59 -raw:ms_level $param_raw_ms_level
60 #end if
61 #if $adv_opts.adv_opts_selector=='advanced':
62 #if $adv_opts.param_force:
63 -force
64 #end if
65 #end if
22 </command> 66 </command>
23 <inputs> 67 <inputs>
24 <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/> 68 <param format="xml,mzml,mzxml,traml,txt,consensusxml" help="(-in) " label="Input files separated by blank" multiple="true" name="param_in" optional="False" size="30" type="data">
25 <param name="param_in_type" type="select" optional="True" label="Input file type (default: determined from file extension or content)" help="(-in_type)"> 69 <sanitizer>
26 <option value="mzData">mzData</option> 70 <valid initial="string.printable">
27 <option value="mzXML">mzXML</option> 71 <remove value="'"/>
28 <option value="mzML">mzML</option> 72 <remove value="&quot;"/>
29 <option value="dta">dta</option> 73 </valid>
30 <option value="dta2d">dta2d</option> 74 </sanitizer>
31 <option value="mgf">mgf</option> 75 </param>
32 <option value="featureXML">featureXML</option> 76 <param checked="false" falsevalue="" help="(-annotate_file_origin) " label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" name="param_annotate_file_origin" optional="True" truevalue="-annotate_file_origin" type="boolean"/>
33 <option value="consensusXML">consensusXML</option> 77 <param help="(-gap) RT concatenation is enabled if a value &gt; 0 is set" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" name="param_rt_concat_gap" type="float" value="0.0"/>
34 <option value="fid">fid</option> 78 <param checked="false" falsevalue="" help="(-rt_auto) " label="Assign retention times automatically (integers starting at 1)" name="param_raw_rt_auto" optional="True" truevalue="-raw:rt_auto" type="boolean"/>
35 <option value="traML">traML</option> 79 <repeat min="0" name="rep_param_raw_rt_custom" title="param_raw_rt_custom">
36 </param> 80 <param help="(-rt_custom) The number of given retention times must be equal to the number of input files" label="List of custom retention times that are assigned to the files" name="param_raw_rt_custom" size="30" type="text" value="0">
37 <param name="param_annotate_file_origin" type="boolean" truevalue="-annotate_file_origin true" falsevalue="-annotate_file_origin false" 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)"/> 81 <sanitizer>
38 <param name="param_rt_auto" type="boolean" truevalue="-raw:rt_auto true" falsevalue="-raw:rt_auto false" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto)"/> 82 <valid initial="string.printable">
39 <param name="param_rt_custom" type="text" size="20" value="0" label="List of custom retention times that are assigned to the files. The number of given retention times must be equal to the number of given input file." help="(-rt_custom)"/> 83 <remove value="'"/>
40 <param name="param_rt_filename" type="boolean" truevalue="-raw:rt_filename true" falsevalue="-raw:rt_filename false" checked="false" optional="True" label="If this flag is set FileMerger tries to guess the rt of the file name.#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" help="(-rt_filename)"/> 84 <remove value="&quot;"/>
41 <param name="param_ms_level" type="integer" value="2" label="This option is useful for use with DTA files which does not contain MS level information. The given level is assigned to the spectra." help="(-ms_level)"/> 85 </valid>
42 <param name="param_user_ms_level" type="boolean" truevalue="-raw:user_ms_level true" falsevalue="-raw:user_ms_level false" checked="false" optional="True" label="If this flag is set, the MS level given above is used" help="(-user_ms_level)"/> 86 </sanitizer>
43 </inputs> 87 </param>
44 <outputs> 88 </repeat>
45 <data name="param_out" label="Output file" format="consensusXML"> 89 <param checked="false" falsevalue="" help="(-rt_filename) e.g. 'my_spectrum_rt2795.15.dta'" 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," name="param_raw_rt_filename" optional="True" truevalue="-raw:rt_filename" type="boolean"/>
46 <change_format> 90 <param help="(-ms_level) This option is useful for DTA files which do not contain MS level information" label="If 1 or higher, this number is assigned to spectra as the MS level" name="param_raw_ms_level" type="integer" value="0"/>
47 <when input="param_out_type" value="mzML" format="mzML"/> 91 <expand macro="advanced_options">
48 <when input="param_out_type" value="featureXML" format="featureXML"/> 92 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
49 </change_format> 93 </expand>
50 </data> 94 </inputs>
51 </outputs> 95 <outputs>
52 <help>**What it does** 96 <data format="xml" name="param_out"/>
53 97 <!--<data format="trafoxml" name="param_rt_concat_trafo_out"/>-->
54 Merges several MS files into one file. 98 </outputs>
99 <help>Merges several MS files into one file.
55 100
56 101
57 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html 102 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html</help>
58 103 </tool>
59 @REFERENCES@
60 </help>
61 </tool>