Mercurial > repos > galaxyp > openms_speclibcreator

comparison SpecLibCreator.xml @ 9:70105532a580 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 20:00:46 +0000
parents 1ea89972c6c7
children 5d837ca93d0e
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8:f2d11c4b5298 9:70105532a580
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="SpecLibCreator" name="SpecLibCreator" version="2.3.0"> 4 <tool id="SpecLibCreator" name="SpecLibCreator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Creates an MSP formatted spectral library.</description> 5 <description>Creates an MSP formatted spectral library.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SpecLibCreator</token> 7 <token name="@EXECUTABLE@">SpecLibCreator</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[SpecLibCreator 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_info: 18 ## Preprocessing
16 -info $param_info 19 mkdir info &&
17 #end if 20 ln -s '$info' 'info/${re.sub("[^\w\-_]", "_", $info.element_identifier)}.$gxy2omsext($info.ext)' &&
18 #if $param_itemseperator: 21 mkdir spec &&
19 -itemseperator "$param_itemseperator" 22 ln -s '$spec' 'spec/${re.sub("[^\w\-_]", "_", $spec.element_identifier)}.$gxy2omsext($spec.ext)' &&
20 #end if 23 mkdir out &&
21 #if $param_itemenclosed: 24
22 -itemenclosed 25 ## Main program call
23 #end if 26
24 #if $param_spec: 27 set -o pipefail &&
25 -spec $param_spec 28 @EXECUTABLE@ -write_ctd ./ &&
26 #end if 29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
27 #if $param_out: 30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
28 -out $param_out 31 -info
29 #end if 32 'info/${re.sub("[^\w\-_]", "_", $info.element_identifier)}.$gxy2omsext($info.ext)'
30 #if $adv_opts.adv_opts_selector=='advanced': 33 -spec
31 #if $adv_opts.param_force: 34 'spec/${re.sub("[^\w\-_]", "_", $spec.element_identifier)}.$gxy2omsext($spec.ext)'
32 -force 35 -out
33 #end if 36 'out/output.${gxy2omsext("msp")}'
34 #end if 37
35 ]]></command> 38 ## Postprocessing
39 && mv 'out/output.${gxy2omsext("msp")}' '$out'
40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
42 #end if]]></command>
43 <configfiles>
44 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles>
36 <inputs> 47 <inputs>
37 <param name="param_info" type="data" format="tabular" optional="False" label="Holds id, peptide, retention time etc" help="(-info) "/> 48 <param name="info" argument="-info" type="data" format="csv" optional="false" label="Holds id, peptide, retention time etc" help=" select csv data sets(s)"/>
38 <param name="param_itemseperator" type="text" size="30" value="," label=" Separator between items. e.g. ," help="(-itemseperator) "> 49 <param name="itemseperator" argument="-itemseperator" type="text" optional="true" value="," label=" Separator between items. e.g. ," help="">
39 <sanitizer> 50 <expand macro="list_string_san"/>
40 <valid initial="string.printable">
41 <remove value="'"/>
42 <remove value="&quot;"/>
43 </valid>
44 </sanitizer>
45 </param> 51 </param>
46 <param name="param_itemenclosed" display="radio" type="boolean" truevalue="-itemenclosed" falsevalue="" checked="false" optional="True" label="'true' or 'false' if true every item is enclosed" help="(-itemenclosed) e.g. '$peptide$,$run$"/> 52 <param name="itemenclosed" argument="-itemenclosed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="'true' or 'false' if true every item is enclosed" help="e.g. '$peptide$,$run$"/>
47 <param name="param_spec" type="data" format="mzData,mzxml" optional="False" label="spectra" help="(-spec) "/> 53 <param name="spec" argument="-spec" type="data" format="mzdata,mzxml" optional="false" label="spectra" help=" select mzdata,mzxml data sets(s)"/>
48 <expand macro="advanced_options"> 54 <expand macro="adv_opts_macro">
49 <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>
50 </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>
51 </inputs> 63 </inputs>
52 <outputs> 64 <outputs>
53 <data name="param_out" format="msp"/> 65 <data name="out" label="${tool.name} on ${on_string}: out" format="msp"/>
66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
68 </data>
54 </outputs> 69 </outputs>
55 <help>Creates an MSP formatted spectral library. 70 <tests>
71 <expand macro="autotest_SpecLibCreator"/>
72 <expand macro="manutest_SpecLibCreator"/>
73 </tests>
74 <help><![CDATA[Creates an MSP formatted spectral library.
56 75
57 76
58 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SpecLibCreator.html</help> 77 For more information, visit http://www.openms.de/documentation/UTILS_SpecLibCreator.html]]></help>
78 <expand macro="references"/>
59 </tool> 79 </tool>