Mercurial > repos > galaxyp > openms_ticcalculator
comparison TICCalculator.xml @ 9:32667824b653 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 16:16:16 +0000 |
parents | 488ea525e0b1 |
children | ed6c05e730de |
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8:60d1971a0cf4 | 9:32667824b653 |
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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: [Utilities]--> | 3 <!--Proposed Tool Section: [Utilities]--> |
4 <tool id="TICCalculator" name="TICCalculator" version="2.3.0"> | 4 <tool id="TICCalculator" name="TICCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description> | 5 <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">TICCalculator</token> | 7 <token name="@EXECUTABLE@">TICCalculator</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[TICCalculator | 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 $param_read_method: | 21 |
19 -read_method | 22 ## Main program call |
20 #if " " in str($param_read_method): | 23 |
21 "$param_read_method" | 24 set -o pipefail && |
22 #else | 25 @EXECUTABLE@ -write_ctd ./ && |
23 $param_read_method | 26 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
24 #end if | 27 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
25 #end if | 28 -in |
26 #if $param_loadData: | 29 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
27 -loadData | 30 | tee '$stdout' |
28 #if " " in str($param_loadData): | 31 |
29 "$param_loadData" | 32 ## Postprocessing |
30 #else | 33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
31 $param_loadData | 34 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
32 #end if | 35 #end if]]></command> |
33 #end if | 36 <configfiles> |
34 #if $adv_opts.adv_opts_selector=='advanced': | 37 <inputs name="args_json" data_style="paths"/> |
35 #if $adv_opts.param_force: | 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
36 -force | 39 </configfiles> |
37 #end if | |
38 #end if | |
39 > $param_stdout | |
40 ]]></command> | |
41 <inputs> | 40 <inputs> |
42 <param name="param_in" type="data" format="mzData,mzxml,mzml,cachedMzML,dta,dta2d,mgf,featurexml,consensusxml,ms2,fid,tabular,peplist,kroenik,tabular" optional="False" label="Input file to convert" help="(-in) "/> | 41 <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/> |
43 <param name="param_read_method" type="select" optional="False" value="regular" label="Method to read the file" help="(-read_method) "> | 42 <param name="read_method" argument="-read_method" type="select" optional="false" label="Method to read the file" help=""> |
44 <option value="regular" selected="true">regular</option> | 43 <option value="regular" selected="true">regular</option> |
45 <option value="indexed">indexed</option> | 44 <option value="indexed">indexed</option> |
46 <option value="indexed_parallel">indexed_parallel</option> | 45 <option value="indexed_parallel">indexed_parallel</option> |
47 <option value="streaming">streaming</option> | 46 <option value="streaming">streaming</option> |
48 <option value="cached">cached</option> | 47 <option value="cached">cached</option> |
49 <option value="cached_parallel">cached_parallel</option> | 48 <option value="cached_parallel">cached_parallel</option> |
49 <expand macro="list_string_san"/> | |
50 </param> | 50 </param> |
51 <param name="param_loadData" display="radio" type="select" optional="False" value="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help="(-loadData) "> | 51 <param name="loadData" argument="-loadData" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help=""/> |
52 <option value="true" selected="true">true</option> | 52 <expand macro="adv_opts_macro"> |
53 <option value="false">false</option> | 53 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> |
54 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
55 <expand macro="list_string_san"/> | |
56 </param> | |
57 </expand> | |
58 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
54 </param> | 60 </param> |
55 <expand macro="advanced_options"> | |
56 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
57 </expand> | |
58 </inputs> | 61 </inputs> |
59 <outputs> | 62 <outputs> |
60 <data name="param_stdout" format="txt" label="Output from stdout"/> | 63 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> |
64 <filter>OPTIONAL_OUTPUTS is None</filter> | |
65 </data> | |
66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
68 </data> | |
61 </outputs> | 69 </outputs> |
62 <help>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking). | 70 <tests> |
71 <expand macro="autotest_TICCalculator"/> | |
72 <expand macro="manutest_TICCalculator"/> | |
73 </tests> | |
74 <help><![CDATA[Calculates the TIC from a mass spectrometric raw file (useful for benchmarking). | |
63 | 75 |
64 | 76 |
65 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_TICCalculator.html</help> | 77 For more information, visit http://www.openms.de/documentation/UTILS_TICCalculator.html]]></help> |
78 <expand macro="references"/> | |
66 </tool> | 79 </tool> |