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comparison DTAExtractor.xml @ 13:e31fe5424cbe draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:22:25 +0000
parents fd0630ab8463
children d8b1ec05fbd7
comparison
equal deleted inserted replaced
12:d29cd605bb48 13:e31fe5424cbe
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="DTAExtractor" name="DTAExtractor" version="2.3.0"> 4 <tool id="DTAExtractor" name="DTAExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Extracts spectra of an MS run file to several files in DTA format.</description> 5 <description>Extracts spectra of an MS run file to several files in DTA format.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">DTAExtractor</token> 7 <token name="@EXECUTABLE@">DTAExtractor</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[DTAExtractor 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21
19 -out "$param_out" 22 ## Main program call
20 #end if 23
21 #if $param_mz: 24 set -o pipefail &&
22 -mz "$param_mz" 25 @EXECUTABLE@ -write_ctd ./ &&
23 #end if 26 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
24 #if $param_rt: 27 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
25 -rt "$param_rt" 28 -in
26 #end if 29 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
27 #if $param_level: 30 | tee '$stdout'
28 -level "$param_level" 31
29 #end if 32 ## Postprocessing
30 #if $adv_opts.adv_opts_selector=='advanced': 33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
31 #if $adv_opts.param_force: 34 && mv '@EXECUTABLE@.ctd' '$ctd_out'
32 -force 35 #end if]]></command>
33 #end if 36 <configfiles>
34 #end if 37 <inputs name="args_json" data_style="paths"/>
35 &gt; $param_stdout 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
36 ]]></command> 39 </configfiles>
37 <inputs> 40 <inputs>
38 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> 41 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
39 <param name="param_out" type="text" size="30" label="base name of DTA output files (RT, m/z and extension are appended)" help="(-out) "> 42 <param name="out" argument="-out" type="text" optional="false" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
40 <sanitizer> 43 <expand macro="list_string_san"/>
41 <valid initial="string.printable">
42 <remove value="'"/>
43 <remove value="&quot;"/>
44 </valid>
45 </sanitizer>
46 </param> 44 </param>
47 <param name="param_mz" type="text" size="30" value=":" label="m/z range of precursor peaks to extract" help="(-mz) &lt;br&gt;This option is ignored for MS level 1"> 45 <param name="mz" argument="-mz" type="text" optional="true" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
48 <sanitizer> 46 <expand macro="list_string_san"/>
49 <valid initial="string.printable">
50 <remove value="'"/>
51 <remove value="&quot;"/>
52 </valid>
53 </sanitizer>
54 </param> 47 </param>
55 <param name="param_rt" type="text" size="30" value=":" label="retention time range of spectra to extract" help="(-rt) "> 48 <param name="rt" argument="-rt" type="text" optional="true" value=":" label="retention time range of spectra to extract" help="">
56 <sanitizer> 49 <expand macro="list_string_san"/>
57 <valid initial="string.printable">
58 <remove value="'"/>
59 <remove value="&quot;"/>
60 </valid>
61 </sanitizer>
62 </param> 50 </param>
63 <param name="param_level" type="text" size="30" value="1,2,3" label="MS levels to extract" help="(-level) "> 51 <param name="level" argument="-level" type="text" optional="true" value="1,2,3" label="MS levels to extract" help="">
64 <sanitizer> 52 <expand macro="list_string_san"/>
65 <valid initial="string.printable">
66 <remove value="'"/>
67 <remove value="&quot;"/>
68 </valid>
69 </sanitizer>
70 </param> 53 </param>
71 <expand macro="advanced_options"> 54 <expand macro="adv_opts_macro">
72 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 55 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
56 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
57 <expand macro="list_string_san"/>
58 </param>
73 </expand> 59 </expand>
60 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
62 </param>
74 </inputs> 63 </inputs>
75 <outputs> 64 <outputs>
76 <data name="param_stdout" format="txt" label="Output from stdout"/> 65 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
66 <filter>OPTIONAL_OUTPUTS is None</filter>
67 </data>
68 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
69 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
70 </data>
77 </outputs> 71 </outputs>
78 <help>Extracts spectra of an MS run file to several files in DTA format. 72 <tests>
73 <expand macro="autotest_DTAExtractor"/>
74 <expand macro="manutest_DTAExtractor"/>
75 </tests>
76 <help><![CDATA[Extracts spectra of an MS run file to several files in DTA format.
79 77
80 78
81 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_DTAExtractor.html</help> 79 For more information, visit http://www.openms.de/documentation/TOPP_DTAExtractor.html]]></help>
80 <expand macro="references"/>
82 </tool> 81 </tool>