Mercurial > repos > galaxyp > openms_spectrafilterthresholdmower
comparison SpectraFilterThresholdMower.xml @ 9:e9ec21114394 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
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date | Thu, 03 Sep 2020 16:20:19 +0000 |
parents | 11697470e19a |
children | dd4ae875c004 |
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8:35d0d5f4e210 | 9:e9ec21114394 |
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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: [Identification]--> | 3 <!--Proposed Tool Section: [Identification]--> |
4 <tool id="SpectraFilterThresholdMower" name="SpectraFilterThresholdMower" version="2.3.0"> | 4 <tool id="SpectraFilterThresholdMower" name="SpectraFilterThresholdMower" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Applies thresholdfilter to peak spectra.</description> | 5 <description>Applies thresholdfilter to peak spectra.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">SpectraFilterThresholdMower</token> | 7 <token name="@EXECUTABLE@">SpectraFilterThresholdMower</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[SpectraFilterThresholdMower | 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 | 22 |
20 #end if | 23 ## Main program call |
21 #if $param_algorithm_threshold: | 24 |
22 -algorithm:threshold $param_algorithm_threshold | 25 set -o pipefail && |
23 #end if | 26 @EXECUTABLE@ -write_ctd ./ && |
24 #if $adv_opts.adv_opts_selector=='advanced': | 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
25 #if $adv_opts.param_force: | 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
26 -force | 29 -in |
27 #end if | 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
28 #end if | 31 -out |
29 ]]></command> | 32 'out/output.${gxy2omsext("mzml")}' |
33 | |
34 ## Postprocessing | |
35 && mv 'out/output.${gxy2omsext("mzml")}' '$out' | |
36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS | |
37 && mv '@EXECUTABLE@.ctd' '$ctd_out' | |
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> | |
30 <inputs> | 43 <inputs> |
31 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> | 44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> |
32 <param name="param_algorithm_threshold" type="float" value="0.05" label="Intensity threshold, peaks below this threshold are discarded" help="(-threshold) "/> | 45 <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false"> |
33 <expand macro="advanced_options"> | 46 <param name="threshold" argument="-algorithm:threshold" type="float" optional="true" value="0.05" label="Intensity threshold, peaks below this threshold are discarded" help=""/> |
34 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | 47 </section> |
48 <expand macro="adv_opts_macro"> | |
49 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | |
50 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
51 <expand macro="list_string_san"/> | |
52 </param> | |
35 </expand> | 53 </expand> |
54 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
55 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
56 </param> | |
36 </inputs> | 57 </inputs> |
37 <outputs> | 58 <outputs> |
38 <data name="param_out" format="mzml"/> | 59 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
60 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
61 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
62 </data> | |
39 </outputs> | 63 </outputs> |
40 <help>Applies thresholdfilter to peak spectra. | 64 <tests> |
65 <expand macro="autotest_SpectraFilterThresholdMower"/> | |
66 <expand macro="manutest_SpectraFilterThresholdMower"/> | |
67 </tests> | |
68 <help><![CDATA[Applies thresholdfilter to peak spectra. | |
41 | 69 |
42 | 70 |
43 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_SpectraFilterThresholdMower.html</help> | 71 For more information, visit http://www.openms.de/documentation/TOPP_SpectraFilterThresholdMower.html]]></help> |
72 <expand macro="references"/> | |
44 </tool> | 73 </tool> |