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comparison FileInfo.xml @ 11:98f171dab07c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:52:57 +0000
parents 92922182d423
children e8dce5e07fa5
comparison
equal deleted inserted replaced
10:febd569ad26f 11:98f171dab07c
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 CTDConverter.--> 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="FileInfo" name="FileInfo" version="2.3.0"> 4 <tool id="FileInfo" name="FileInfo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Shows basic information about the file, such as data ranges and file type.</description> 5 <description>Shows basic information about the file, such as data ranges and file type.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FileInfo</token> 7 <token name="@EXECUTABLE@">FileInfo</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[FileInfo 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir out &&
22 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir out_tsv &&
17 #end if 24 #end if
18 #if $param_out: 25
19 -out $param_out 26 ## Main program call
27
28 set -o pipefail &&
29 @EXECUTABLE@ -write_ctd ./ &&
30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
32 -in
33 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
34 -out
35 'out/output.${gxy2omsext("txt")}'
36 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
37 -out_tsv
38 'out_tsv/output.${gxy2omsext("csv")}'
20 #end if 39 #end if
21 #if $param_out_tsv: 40 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
22 -out_tsv $param_out_tsv 41 | tee '$stdout'
23 #end if 42 #end if
24 #if $param_m: 43
25 -m 44 ## Postprocessing
45 && mv 'out/output.${gxy2omsext("txt")}' '$out'
46 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
47 && mv 'out_tsv/output.${gxy2omsext("csv")}' '$out_tsv'
26 #end if 48 #end if
27 #if $param_p: 49 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
28 -p 50 && mv '@EXECUTABLE@.ctd' '$ctd_out'
29 #end if 51 #end if]]></command>
30 #if $param_s: 52 <configfiles>
31 -s 53 <inputs name="args_json" data_style="paths"/>
32 #end if 54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
33 #if $param_d: 55 </configfiles>
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 #if $adv_opts.adv_opts_selector=='advanced':
46 #if $adv_opts.param_force:
47 -force
48 #end if
49 #end if
50 ]]></command>
51 <inputs> 56 <inputs>
52 <param name="param_in" type="data" format="mzData,mzxml,mzml,dta,dta2d,mgf,featurexml,consensusxml,idxml,pepxml,fid,mzid,trafoxml,fasta" optional="False" label="input file" help="(-in) "/> 57 <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,trafoxml" optional="false" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,trafoxml data sets(s)"/>
53 <param name="param_m" display="radio" type="boolean" truevalue="-m" falsevalue="" checked="false" optional="True" label="Show meta information about the whole experiment" help="(-m) "/> 58 <param name="m" argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
54 <param name="param_p" display="radio" type="boolean" truevalue="-p" falsevalue="" checked="false" optional="True" label="Shows data processing information" help="(-p) "/> 59 <param name="p" argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
55 <param name="param_s" display="radio" type="boolean" truevalue="-s" falsevalue="" checked="false" optional="True" label="Computes a five-number statistics of intensities, qualities, and widths" help="(-s) "/> 60 <param name="s" argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/>
56 <param name="param_d" display="radio" type="boolean" truevalue="-d" falsevalue="" checked="false" optional="True" label="Show detailed listing of all spectra and chromatograms (peak files only)" help="(-d) "/> 61 <param name="d" argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/>
57 <param name="param_c" display="radio" type="boolean" truevalue="-c" falsevalue="" checked="false" optional="True" label="Check for corrupt data in the file (peak files only)" help="(-c) "/> 62 <param name="c" argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/>
58 <param name="param_v" display="radio" type="boolean" truevalue="-v" falsevalue="" checked="false" optional="True" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help="(-v) "/> 63 <param name="v" argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/>
59 <param name="param_i" display="radio" type="boolean" truevalue="-i" falsevalue="" checked="false" optional="True" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help="(-i) "/> 64 <param name="i" argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/>
60 <expand macro="advanced_options"> 65 <expand macro="adv_opts_macro">
61 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 66 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
67 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
68 <expand macro="list_string_san"/>
69 </param>
62 </expand> 70 </expand>
71 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
72 <option value="out_tsv_FLAG">out_tsv (Enables the test mode (needed for internal use only))</option>
73 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
74 </param>
63 </inputs> 75 </inputs>
64 <outputs> 76 <outputs>
65 <data name="param_out" format="txt"/> 77 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
66 <data name="param_out_tsv" format="tabular"/> 78 <data name="out_tsv" label="${tool.name} on ${on_string}: out_tsv" format="csv">
79 <filter>OPTIONAL_OUTPUTS is not None and "out_tsv_FLAG" in OPTIONAL_OUTPUTS</filter>
80 </data>
81 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
82 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
83 </data>
67 </outputs> 84 </outputs>
68 <help>Shows basic information about the file, such as data ranges and file type. 85 <tests>
86 <expand macro="autotest_FileInfo"/>
87 <expand macro="manutest_FileInfo"/>
88 </tests>
89 <help><![CDATA[Shows basic information about the file, such as data ranges and file type.
69 90
70 91
71 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FileInfo.html</help> 92 For more information, visit http://www.openms.de/documentation/TOPP_FileInfo.html]]></help>
93 <expand macro="references"/>
72 </tool> 94 </tool>