Mercurial > repos > galaxyp > openms_psmfeatureextractor
comparison PSMFeatureExtractor.xml @ 4:8d4b175e06b5 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 16:20:56 +0000 |
parents | 54ff34feb43d |
children | 151e4b119c70 |
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3:2bbe01546e77 | 4:8d4b175e06b5 |
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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="PSMFeatureExtractor" name="PSMFeatureExtractor" version="2.3.0"> | 4 <tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Computes extra features for each input PSM.</description> | 5 <description>Computes extra features for each input PSM.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">PSMFeatureExtractor</token> | 7 <token name="@EXECUTABLE@">PSMFeatureExtractor</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[PSMFeatureExtractor | 15 @EXT_FOO@ |
16 #import re | |
14 | 17 |
18 ## Preprocessing | |
19 mkdir in && | |
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } | |
21 mkdir out && | |
22 | |
23 ## Main program call | |
24 | |
25 set -o pipefail && | |
26 @EXECUTABLE@ -write_ctd ./ && | |
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
15 -in | 29 -in |
16 #for token in $param_in: | 30 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} |
17 $token | 31 -out |
18 #end for | 32 'out/output.${out_type}' |
19 #if $param_out: | |
20 -out $param_out | |
21 #end if | |
22 | 33 |
23 #if $rep_param_extra: | 34 ## Postprocessing |
24 -extra | 35 && mv 'out/output.${out_type}' '$out' |
25 #for token in $rep_param_extra: | 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
26 #if " " in str(token): | 37 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
27 "$token.param_extra" | 38 #end if]]></command> |
28 #else | 39 <configfiles> |
29 $token.param_extra | 40 <inputs name="args_json" data_style="paths"/> |
30 #end if | 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
31 #end for | 42 </configfiles> |
32 #end if | |
33 #if $param_multiple_search_engines: | |
34 -multiple_search_engines | |
35 #end if | |
36 #if $adv_opts.adv_opts_selector=='advanced': | |
37 #if $adv_opts.param_skip_db_check: | |
38 -skip_db_check | |
39 #end if | |
40 #if $adv_opts.param_concat: | |
41 -concat | |
42 #end if | |
43 #if $adv_opts.param_impute: | |
44 -impute | |
45 #end if | |
46 #if $adv_opts.param_limit_imputation: | |
47 -limit_imputation | |
48 #end if | |
49 #if $adv_opts.param_force: | |
50 -force | |
51 #end if | |
52 #end if | |
53 ]]></command> | |
54 <inputs> | 43 <inputs> |
55 <param name="param_in" type="data" format="mzid,idxml" multiple="true" optional="False" size="30" label="Input file(s)" help="(-in) "> | 44 <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/> |
56 <sanitizer> | 45 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help=""> |
57 <valid initial="string.printable"> | 46 <option value="idXML">idxml</option> |
58 <remove value="'"/> | 47 <option value="mzid">mzid</option> |
59 <remove value="""/> | 48 <expand macro="list_string_san"/> |
60 </valid> | |
61 </sanitizer> | |
62 </param> | 49 </param> |
63 <repeat name="rep_param_extra" min="0" title="param_extra"> | 50 <param name="extra" argument="-extra" type="text" optional="true" value="" label="List of the MetaData parameters to be included in a feature set for precolato" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
64 <param name="param_extra" type="text" size="30" label="List of the MetaData parameters to be included in a feature set for precolato" help="(-extra) "> | 51 <expand macro="list_string_val"/> |
65 <sanitizer> | 52 <expand macro="list_string_san"/> |
66 <valid initial="string.printable"> | 53 </param> |
67 <remove value="'"/> | 54 <param name="multiple_search_engines" argument="-multiple_search_engines" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Combine PSMs from different search engines by merging on scan level" help=""/> |
68 <remove value="""/> | 55 <expand macro="adv_opts_macro"> |
69 </valid> | 56 <param name="skip_db_check" argument="-skip_db_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Manual override to skip the check if same settings for multiple search engines were applied" help="Only valid together with -multiple_search_engines flag"/> |
70 </sanitizer> | 57 <param name="concat" argument="-concat" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="Only valid together with -multiple_search_engines flag"/> |
58 <param name="impute" argument="-impute" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="Only valid together with -multiple_search_engines flag"/> | |
59 <param name="limit_imputation" argument="-limit_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="Only valid together with -multiple_search_engines flag"/> | |
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"/> | |
71 </param> | 63 </param> |
72 </repeat> | |
73 <param name="param_multiple_search_engines" display="radio" type="boolean" truevalue="-multiple_search_engines" falsevalue="" checked="false" optional="True" label="Combine PSMs from different search engines by merging on scan level" help="(-multiple_search_engines) "/> | |
74 <expand macro="advanced_options"> | |
75 <param name="param_skip_db_check" display="radio" type="boolean" truevalue="-skip_db_check" falsevalue="" checked="false" optional="True" label="Manual override to skip the check if same settings for multiple search engines were applied" help="(-skip_db_check) Only valid together with -multiple_search_engines flag"/> | |
76 <param name="param_concat" display="radio" type="boolean" truevalue="-concat" falsevalue="" checked="false" optional="True" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="(-concat) Only valid together with -multiple_search_engines flag"/> | |
77 <param name="param_impute" display="radio" type="boolean" truevalue="-impute" falsevalue="" checked="false" optional="True" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="(-impute) Only valid together with -multiple_search_engines flag"/> | |
78 <param name="param_limit_imputation" display="radio" type="boolean" truevalue="-limit_imputation" falsevalue="" checked="false" optional="True" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="(-limit_imputation) Only valid together with -multiple_search_engines flag"/> | |
79 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
80 </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> | |
81 </inputs> | 68 </inputs> |
82 <outputs> | 69 <outputs> |
83 <data name="param_out" metadata_source="param_in" format="input"/> | 70 <data name="out" label="${tool.name} on ${on_string}: out"> |
71 <change_format> | |
72 <when input="out_type" value="idXML" format="idxml"/> | |
73 <when input="out_type" value="mzid" format="mzid"/> | |
74 </change_format> | |
75 </data> | |
76 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
77 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
78 </data> | |
84 </outputs> | 79 </outputs> |
85 <help>Computes extra features for each input PSM. | 80 <tests> |
81 <expand macro="autotest_PSMFeatureExtractor"/> | |
82 <expand macro="manutest_PSMFeatureExtractor"/> | |
83 </tests> | |
84 <help><![CDATA[Computes extra features for each input PSM. | |
86 | 85 |
87 | 86 |
88 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_PSMFeatureExtractor.html</help> | 87 For more information, visit http://www.openms.de/documentation/UTILS_PSMFeatureExtractor.html]]></help> |
88 <expand macro="references"/> | |
89 </tool> | 89 </tool> |