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comparison BaselineFilter.xml @ 13:2c6de76669fe draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:36:32 -0400
parents f5946590b034
children 1936361a3dbb
comparison
equal deleted inserted replaced
12:539f9796bd69 13:2c6de76669fe
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="BaselineFilter" name="BaselineFilter" version="2.3.0"> 4 <tool id="BaselineFilter" name="BaselineFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Removes the baseline from profile spectra using a top-hat filter.</description> 5 <description>Removes the baseline from profile spectra using a top-hat filter.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">BaselineFilter</token> 7 <token name="@EXECUTABLE@">BaselineFilter</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[BaselineFilter 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_struc_elem_length: 24
22 -struc_elem_length $param_struc_elem_length 25 set -o pipefail &&
23 #end if 26 @EXECUTABLE@ -write_ctd ./ &&
24 #if $param_struc_elem_unit: 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 -struc_elem_unit 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 #if " " in str($param_struc_elem_unit): 29 -in
27 "$param_struc_elem_unit" 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 #else 31 -out
29 $param_struc_elem_unit 32 'out/output.${gxy2omsext("mzml")}'
30 #end if 33
31 #end if 34 ## Postprocessing
32 #if $param_method: 35 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
33 -method 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 #if " " in str($param_method): 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 "$param_method" 38 #end if]]></command>
36 #else 39 <configfiles>
37 $param_method 40 <inputs name="args_json" data_style="paths"/>
38 #end if 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 #end if 42 </configfiles>
40 #if $adv_opts.adv_opts_selector=='advanced':
41 #if $adv_opts.param_force:
42 -force
43 #end if
44 #end if
45 ]]></command>
46 <inputs> 43 <inputs>
47 <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
48 <param name="param_struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help="(-struc_elem_length) "/> 45 <param name="struc_elem_length" argument="-struc_elem_length" type="float" optional="true" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
49 <param name="param_struc_elem_unit" display="radio" type="select" optional="False" value="Thomson" label="Unit of 'struc_elem_length' paramete" help="(-struc_elem_unit) "> 46 <param name="struc_elem_unit" argument="-struc_elem_unit" display="radio" type="select" optional="false" label="Unit of 'struc_elem_length' paramete" help="">
50 <option value="Thomson" selected="true">Thomson</option> 47 <option value="Thomson" selected="true">Thomson</option>
51 <option value="DataPoints">DataPoints</option> 48 <option value="DataPoints">DataPoints</option>
49 <expand macro="list_string_san"/>
52 </param> 50 </param>
53 <param name="param_method" type="select" optional="False" value="tophat" label="The name of the morphological filter to be applied" help="(-method) If you are unsure, use the default"> 51 <param name="method" argument="-method" type="select" optional="false" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
54 <option value="identity">identity</option> 52 <option value="identity">identity</option>
55 <option value="erosion">erosion</option> 53 <option value="erosion">erosion</option>
56 <option value="dilation">dilation</option> 54 <option value="dilation">dilation</option>
57 <option value="opening">opening</option> 55 <option value="opening">opening</option>
58 <option value="closing">closing</option> 56 <option value="closing">closing</option>
59 <option value="gradient">gradient</option> 57 <option value="gradient">gradient</option>
60 <option value="tophat" selected="true">tophat</option> 58 <option value="tophat" selected="true">tophat</option>
61 <option value="bothat">bothat</option> 59 <option value="bothat">bothat</option>
62 <option value="erosion_simple">erosion_simple</option> 60 <option value="erosion_simple">erosion_simple</option>
63 <option value="dilation_simple">dilation_simple</option> 61 <option value="dilation_simple">dilation_simple</option>
62 <expand macro="list_string_san"/>
64 </param> 63 </param>
65 <expand macro="advanced_options"> 64 <expand macro="adv_opts_macro">
66 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 65 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
66 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
67 <expand macro="list_string_san"/>
68 </param>
67 </expand> 69 </expand>
70 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
71 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
72 </param>
68 </inputs> 73 </inputs>
69 <outputs> 74 <outputs>
70 <data name="param_out" format="mzml"/> 75 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
76 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
77 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
78 </data>
71 </outputs> 79 </outputs>
72 <help>Removes the baseline from profile spectra using a top-hat filter. 80 <tests>
81 <expand macro="autotest_BaselineFilter"/>
82 <expand macro="manutest_BaselineFilter"/>
83 </tests>
84 <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter.
73 85
74 86
75 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_BaselineFilter.html</help> 87 For more information, visit http://www.openms.de/documentation/TOPP_BaselineFilter.html]]></help>
88 <expand macro="references"/>
76 </tool> 89 </tool>