Mercurial > repos > galaxyp > openms_externalcalibration

comparison ExternalCalibration.xml @ 10:4f6a44916c89 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 12:56:06 +0000
parents e57b04faa11a
children 61f5ad339398
comparison
equal deleted inserted replaced
9:e57b04faa11a 10:4f6a44916c89
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: [Signal processing and preprocessing]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="ExternalCalibration" name="ExternalCalibration" version="2.3.0"> 4 <tool id="ExternalCalibration" name="ExternalCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Applies an external mass recalibration.</description> 5 <description>Applies an external mass recalibration.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ExternalCalibration</token> 7 <token name="@EXECUTABLE@">ExternalCalibration</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[ExternalCalibration 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 mkdir out &&
19 -out $param_out
20 #end if
21 #if $param_offset:
22 -offset $param_offset
23 #end if
24 #if $param_slope:
25 -slope $param_slope
26 #end if
27 #if $param_power:
28 -power $param_power
29 #end if
30 22
31 #if $rep_param_ms_level: 23 ## Main program call
32 -ms_level 24
33 #for token in $rep_param_ms_level: 25 set -o pipefail &&
34 #if " " in str(token): 26 @EXECUTABLE@ -write_ctd ./ &&
35 "$token.param_ms_level" 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
36 #else 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
37 $token.param_ms_level 29 -in
38 #end if 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
39 #end for 31 -out
40 #end if 32 'out/output.${gxy2omsext("mzml")}'
41 #if $adv_opts.adv_opts_selector=='advanced': 33
42 #if $adv_opts.param_force: 34 ## Postprocessing
43 -force 35 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
44 #end if 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
45 #end if 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
46 ]]></command> 38 #end if]]></command>
39 <configfiles>
40 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles>
47 <inputs> 43 <inputs>
48 <param name="param_in" type="data" format="mzml" optional="False" label="Input peak file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/>
49 <param name="param_offset" type="float" value="0.0" label="Mass offset in ppm" help="(-offset) "/> 45 <param name="offset" argument="-offset" type="float" optional="true" value="0.0" label="Mass offset in ppm" help=""/>
50 <param name="param_slope" type="float" value="0.0" label="Slope (dependent on m/z)" help="(-slope) "/> 46 <param name="slope" argument="-slope" type="float" optional="true" value="0.0" label="Slope (dependent on m/z)" help=""/>
51 <param name="param_power" type="float" value="0.0" label="Power (dependent on m/z)" help="(-power) "/> 47 <param name="power" argument="-power" type="float" optional="true" value="0.0" label="Power (dependent on m/z)" help=""/>
52 <repeat name="rep_param_ms_level" min="0" max="1" title="param_ms_level"> 48 <param name="ms_level" argument="-ms_level" type="text" optional="true" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Scans with other levels remain unchanged (space separated list, in order to allow for spaces in list items surround them by single quotes)">
53 <param name="param_ms_level" type="text" size="30" value="1 2 3" label="Target MS levels to apply the transformation onto" help="(-ms_level) Scans with other levels remain unchanged"> 49 <expand macro="list_integer_valsan"/>
54 <sanitizer> 50 </param>
55 <valid initial="string.printable"> 51 <expand macro="adv_opts_macro">
56 <remove value="'"/> 52 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
57 <remove value="&quot;"/> 53 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
58 </valid> 54 <expand macro="list_string_san"/>
59 </sanitizer>
60 </param> 55 </param>
61 </repeat>
62 <expand macro="advanced_options">
63 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
64 </expand> 56 </expand>
57 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
59 </param>
65 </inputs> 60 </inputs>
66 <outputs> 61 <outputs>
67 <data name="param_out" format="mzml"/> 62 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
65 </data>
68 </outputs> 66 </outputs>
69 <help>Applies an external mass recalibration. 67 <tests>
68 <expand macro="autotest_ExternalCalibration"/>
69 <expand macro="manutest_ExternalCalibration"/>
70 </tests>
71 <help><![CDATA[Applies an external mass recalibration.
70 72
71 73
72 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ExternalCalibration.html</help> 74 For more information, visit http://www.openms.de/documentation/TOPP_ExternalCalibration.html]]></help>
75 <expand macro="references"/>
73 </tool> 76 </tool>