Mercurial > repos > galaxyp > openms_openswathfilesplitter

comparison OpenSwathFileSplitter.xml @ 9:0ab17cc5cf0c 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 19:55:24 +0000
parents 508e1f473cfe
children 2d856cba192b
comparison
equal deleted inserted replaced
8:8b814eafce2c 9:0ab17cc5cf0c
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathFileSplitter" name="OpenSwathFileSplitter" version="2.3.0"> 4 <tool id="OpenSwathFileSplitter" name="OpenSwathFileSplitter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Splits SWATH files into n files, each containing one window.</description> 5 <description>Splits SWATH files into n files, each containing one window.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathFileSplitter</token> 7 <token name="@EXECUTABLE@">OpenSwathFileSplitter</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[OpenSwathFileSplitter 15 @EXT_FOO@
16 #import re
14 17
18 ## Preprocessing
19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir adv_opts_cond.outputDirectory &&
22 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir out_qc &&
24 #end if
25
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
15 -in 32 -in
16 #for token in $param_in: 33 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
17 $token 34 -outputDirectory
18 #end for 35 adv_opts_cond.outputDirectory/
19 #if $adv_opts.adv_opts_selector=='advanced': 36 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
20 #if $adv_opts.param_outputDirectory: 37 -out_qc
21 -outputDirectory "$adv_opts.param_outputDirectory" 38 'out_qc/output.${gxy2omsext("json")}'
22 #end if 39 #end if
23 #if $adv_opts.param_force: 40 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
24 -force 41 | tee '$stdout'
25 #end if 42 #end if
43
44 ## Postprocessing
45 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
46 && mv 'out_qc/output.${gxy2omsext("json")}' '$out_qc'
26 #end if 47 #end if
27 &gt; $param_stdout 48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
28 ]]></command> 49 && mv '@EXECUTABLE@.ctd' '$ctd_out'
50 #end if]]></command>
51 <configfiles>
52 <inputs name="args_json" data_style="paths"/>
53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
54 </configfiles>
29 <inputs> 55 <inputs>
30 <param name="param_in" type="data" format="mzml,mzxml" multiple="true" optional="False" size="30" label="Input file (SWATH/DIA file)" help="(-in) "> 56 <param name="in" argument="-in" type="data" format="mzml,mzxml" optional="false" label="Input file (SWATH/DIA file)" help=" select mzml,mzxml data sets(s)"/>
31 <sanitizer> 57 <expand macro="adv_opts_macro">
32 <valid initial="string.printable"> 58 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
33 <remove value="'"/> 59 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
34 <remove value="&quot;"/> 60 <expand macro="list_string_san"/>
35 </valid> 61 </param>
36 </sanitizer> 62 </expand>
63 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
64 <option value="out_qc_FLAG">out_qc (Enables the test mode (needed for internal use only))</option>
65 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
37 </param> 66 </param>
38 <expand macro="advanced_options">
39 <param name="param_outputDirectory" type="text" size="30" value="./" label="Output path to store the split files" help="(-outputDirectory) ">
40 <sanitizer>
41 <valid initial="string.printable">
42 <remove value="'"/>
43 <remove value="&quot;"/>
44 </valid>
45 </sanitizer>
46 </param>
47 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
48 </expand>
49 </inputs> 67 </inputs>
50 <outputs> 68 <outputs>
51 <data name="param_stdout" format="txt" label="Output from stdout"/> 69 <collection type="list" name="adv_opts_cond.outputDirectory" label="${tool.name} on ${on_string}: outputDirectory">
70 <discover_datasets directory="adv_opts_cond.outputDirectory" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
71 </collection>
72 <data name="out_qc" label="${tool.name} on ${on_string}: out_qc" format="json">
73 <filter>OPTIONAL_OUTPUTS is not None and "out_qc_FLAG" in OPTIONAL_OUTPUTS</filter>
74 </data>
75 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
76 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
77 </data>
52 </outputs> 78 </outputs>
53 <help>Splits SWATH files into n files, each containing one window. 79 <tests>
80 <expand macro="autotest_OpenSwathFileSplitter"/>
81 <expand macro="manutest_OpenSwathFileSplitter"/>
82 </tests>
83 <help><![CDATA[Splits SWATH files into n files, each containing one window.
54 84
55 85
56 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_OpenSwathFileSplitter.html</help> 86 For more information, visit http://www.openms.de/documentation/UTILS_OpenSwathFileSplitter.html]]></help>
87 <expand macro="references"/>
57 </tool> 88 </tool>