Mercurial > repos > galaxyp > openms_baselinefilter
comparison BaselineFilter.xml @ 13:2c6de76669fe 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, 27 Aug 2020 19:36:32 -0400 |
parents | f5946590b034 |
children | 1936361a3dbb |
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12:539f9796bd69 | 13:2c6de76669fe |
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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: [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> |