Mercurial > repos > galaxyp > openms_consensusmapnormalizer
comparison ConsensusMapNormalizer.xml @ 13:9ff14d340f84 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 20:02:43 +0000 |
parents | f67f3c7c062f |
children | 226f58ac71c5 |
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12:c7af42f1eae5 | 13:9ff14d340f84 |
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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: [Map Alignment]--> | 3 <!--Proposed Tool Section: [Map Alignment]--> |
4 <tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="2.3.0"> | 4 <tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Normalizes maps of one consensusXML file</description> | 5 <description>Normalizes maps of one consensusXML file</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">ConsensusMapNormalizer</token> | 7 <token name="@EXECUTABLE@">ConsensusMapNormalizer</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[ConsensusMapNormalizer | 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 $param_algorithm_type: | 24 |
22 -algorithm_type | 25 set -o pipefail && |
23 #if " " in str($param_algorithm_type): | 26 @EXECUTABLE@ -write_ctd ./ && |
24 "$param_algorithm_type" | 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
25 #else | 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
26 $param_algorithm_type | 29 -in |
27 #end if | 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
28 #end if | 31 -out |
29 #if $param_ratio_threshold: | 32 'out/output.${gxy2omsext("consensusxml")}' |
30 -ratio_threshold $param_ratio_threshold | 33 |
31 #end if | 34 ## Postprocessing |
32 #if $adv_opts.adv_opts_selector=='advanced': | 35 && mv 'out/output.${gxy2omsext("consensusxml")}' '$out' |
33 #if $adv_opts.param_accession_filter: | 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
34 -accession_filter "$adv_opts.param_accession_filter" | 37 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
35 #end if | 38 #end if]]></command> |
36 #if $adv_opts.param_description_filter: | 39 <configfiles> |
37 -description_filter "$adv_opts.param_description_filter" | 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 #if $adv_opts.param_force: | 42 </configfiles> |
40 -force | |
41 #end if | |
42 #end if | |
43 ]]></command> | |
44 <inputs> | 43 <inputs> |
45 <param name="param_in" type="data" format="consensusxml" optional="False" label="input file" help="(-in) "/> | 44 <param name="in" argument="-in" type="data" format="consensusxml" optional="false" label="input file" help=" select consensusxml data sets(s)"/> |
46 <param name="param_algorithm_type" display="radio" type="select" optional="False" value="robust_regression" label="The normalization algorithm that is applied" help="(-algorithm_type) 'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)"> | 45 <param name="algorithm_type" argument="-algorithm_type" display="radio" type="select" optional="false" label="The normalization algorithm that is applied" help="'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)"> |
47 <option value="robust_regression" selected="true">robust_regression</option> | 46 <option value="robust_regression" selected="true">robust_regression</option> |
48 <option value="median">median</option> | 47 <option value="median">median</option> |
49 <option value="median_shift">median_shift</option> | 48 <option value="median_shift">median_shift</option> |
50 <option value="quantile">quantile</option> | 49 <option value="quantile">quantile</option> |
50 <expand macro="list_string_san"/> | |
51 </param> | 51 </param> |
52 <param name="param_ratio_threshold" type="float" min="0.001" max="1.0" optional="True" value="0.67" label="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold < intensity ratio < 1/ratio_threshold) and outliers" help="(-ratio_threshold) "/> | 52 <param name="ratio_threshold" argument="-ratio_threshold" type="float" optional="true" min="0.001" max="1.0" value="0.67" label="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold < intensity ratio < 1/ratio_threshold) and outliers" help=""/> |
53 <expand macro="advanced_options"> | 53 <expand macro="adv_opts_macro"> |
54 <param name="param_accession_filter" type="text" size="30" label="Use only features with accessions (partially) matching this regular expression for computing the normalization factors. Useful," help="(-accession_filter) e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used"> | 54 <param name="accession_filter" argument="-accession_filter" type="text" optional="true" value="" label="Use only features with accessions (partially) matching this regular expression for computing the normalization factors" help="Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used"> |
55 <sanitizer> | 55 <expand macro="list_string_san"/> |
56 <valid initial="string.printable"> | |
57 <remove value="'"/> | |
58 <remove value="""/> | |
59 </valid> | |
60 </sanitizer> | |
61 </param> | 56 </param> |
62 <param name="param_description_filter" type="text" size="30" label="Use only features with description (partially) matching this regular expression for computing the normalization factors. Useful," help="(-description_filter) e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used"> | 57 <param name="description_filter" argument="-description_filter" type="text" optional="true" value="" label="Use only features with description (partially) matching this regular expression for computing the normalization factors" help="Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used"> |
63 <sanitizer> | 58 <expand macro="list_string_san"/> |
64 <valid initial="string.printable"> | |
65 <remove value="'"/> | |
66 <remove value="""/> | |
67 </valid> | |
68 </sanitizer> | |
69 </param> | 59 </param> |
70 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | 60 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> |
61 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
62 <expand macro="list_string_san"/> | |
63 </param> | |
71 </expand> | 64 </expand> |
65 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
66 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
67 </param> | |
72 </inputs> | 68 </inputs> |
73 <outputs> | 69 <outputs> |
74 <data name="param_out" format="consensusxml"/> | 70 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> |
71 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
72 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
73 </data> | |
75 </outputs> | 74 </outputs> |
76 <help>Normalizes maps of one consensusXML file | 75 <tests> |
76 <expand macro="autotest_ConsensusMapNormalizer"/> | |
77 <expand macro="manutest_ConsensusMapNormalizer"/> | |
78 </tests> | |
79 <help><![CDATA[Normalizes maps of one consensusXML file | |
77 | 80 |
78 | 81 |
79 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ConsensusMapNormalizer.html</help> | 82 For more information, visit http://www.openms.de/documentation/TOPP_ConsensusMapNormalizer.html]]></help> |
83 <expand macro="references"/> | |
80 </tool> | 84 </tool> |