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comparison FileInfo.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="FileInfo" name="FileInfo" 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>Shows basic information about the file, such as data ranges and file type.</description> 3 <!--Proposed Tool Section: [File Handling]-->
4 <macros> 4 <tool id="FileInfo" name="FileInfo" version="2.0.0">
5 <token name="@EXECUTABLE@">FileInfo</token> 5 <description>Shows basic information about the file, such as data ranges and file type.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">FileInfo</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>FileInfo 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FileInfo
11 14
12 -in ${param_in} 15 #if $param_in:
13 -in_type ${param_in_type} 16 -in $param_in
14 -out ${param_out} 17 #end if
15 ${param_m} 18 #if $param_out:
16 ${param_p} 19 -out $param_out
17 ${param_s} 20 #end if
18 ${param_d} 21 #if $param_out_tsv:
19 ${param_c} 22 -out_tsv $param_out_tsv
20 ${param_v} 23 #end if
21 ${param_i} 24 #if $param_m:
22 -threads \${GALAXY_SLOTS:-24} 25 -m
26 #end if
27 #if $param_p:
28 -p
29 #end if
30 #if $param_s:
31 -s
32 #end if
33 #if $param_d:
34 -d
35 #end if
36 #if $param_c:
37 -c
38 #end if
39 #if $param_v:
40 -v
41 #end if
42 #if $param_i:
43 -i
44 #end if
45 -threads \${GALAXY_SLOTS:-24}
23 #if $adv_opts.adv_opts_selector=='advanced': 46 #if $adv_opts.adv_opts_selector=='advanced':
24 -out_tsv ${adv_opts.param_out_tsv} 47 #if $adv_opts.param_force:
48 -force
49 #end if
25 #end if 50 #end if
26 </command> 51 </command>
27 <inputs> 52 <inputs>
28 <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML,idXML,pepXML" optional="False" label="input file " help="(-in)"/> 53 <param format="xml,mzml,mzxml,consensusxml,txt,pepxml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
29 <param name="param_in_type" type="select" optional="True" label="input file type -- default: determined from file extension or content" help="(-in_type)"> 54 <param checked="false" falsevalue="" help="(-m) " label="Show meta information about the whole experiment" name="param_m" optional="True" truevalue="-m" type="boolean"/>
30 <option value="mzData">mzData</option> 55 <param checked="false" falsevalue="" help="(-p) " label="Shows data processing information" name="param_p" optional="True" truevalue="-p" type="boolean"/>
31 <option value="mzXML">mzXML</option> 56 <param checked="false" falsevalue="" help="(-s) " label="Computes a five-number statistics of intensities, qualities, and widths" name="param_s" optional="True" truevalue="-s" type="boolean"/>
32 <option value="mzML">mzML</option> 57 <param checked="false" falsevalue="" help="(-d) " label="Show detailed listing of all spectra and chromatograms (peak files only)" name="param_d" optional="True" truevalue="-d" type="boolean"/>
33 <option value="dta">dta</option> 58 <param checked="false" falsevalue="" help="(-c) " label="Check for corrupt data in the file (peak files only)" name="param_c" optional="True" truevalue="-c" type="boolean"/>
34 <option value="dta2d">dta2d</option> 59 <param checked="false" falsevalue="" help="(-v) " label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" name="param_v" optional="True" truevalue="-v" type="boolean"/>
35 <option value="mgf">mgf</option> 60 <param checked="false" falsevalue="" help="(-i) " label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" name="param_i" optional="True" truevalue="-i" type="boolean"/>
36 <option value="featureXML">featureXML</option> 61 <expand macro="advanced_options">
37 <option value="consensusXML">consensusXML</option> 62 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
38 <option value="idXML">idXML</option> 63 </expand>
39 <option value="pepXML">pepXML</option> 64 </inputs>
40 <option value="fid">fid</option> 65 <outputs>
41 </param> 66 <data format="txt" name="param_out"/>
42 <param name="param_m" type="boolean" truevalue="-m true" falsevalue="-m false" checked="false" optional="True" label="Show meta information about the whole experiment" help="(-m)"/> 67 <data format="tabular" name="param_out_tsv"/>
43 <param name="param_p" type="boolean" truevalue="-p true" falsevalue="-p false" checked="false" optional="True" label="Shows data processing information" help="(-p)"/> 68 </outputs>
44 <param name="param_s" type="boolean" truevalue="-s true" falsevalue="-s false" checked="false" optional="True" label="Computes a five-number statistics of intensities, qualities, and widths" help="(-s)"/> 69 <help>Shows basic information about the file, such as data ranges and file type.
45 <param name="param_d" type="boolean" truevalue="-d true" falsevalue="-d false" checked="false" optional="True" label="Show detailed listing of all spectra and chromatograms (peak files only)" help="(-d)"/>
46 <param name="param_c" type="boolean" truevalue="-c true" falsevalue="-c false" checked="false" optional="True" label="Check for corrupt data in the file (peak files only)" help="(-c)"/>
47 <param name="param_v" type="boolean" truevalue="-v true" falsevalue="-v false" checked="false" optional="True" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help="(-v)"/>
48 <param name="param_i" type="boolean" truevalue="-i true" falsevalue="-i false" checked="false" optional="True" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help="(-i)"/>
49 </inputs>
50 <outputs>
51 <data name="param_out" label="Optional output file. If left out, the output is written to the command line." format="txt"/>
52 <data name="param_out_tsv" label="Second optional output file. Tab separated flat text file." format="tabular"/>
53 </outputs>
54 <help>**What it does**
55
56 Shows basic information about the file, such as data ranges and file type.
57 70
58 71
59 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileInfo.html 72 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileInfo.html</help>
60 73 </tool>
61 @REFERENCES@
62 </help>
63 </tool>