Mercurial > repos > galaxyp > openms_ticcalculator

comparison TICCalculator.xml @ 9:32667824b653 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:16:16 +0000
parents 488ea525e0b1
children ed6c05e730de
comparison
equal deleted inserted replaced
8:60d1971a0cf4 9:32667824b653
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 &gt; $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>