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comparison PSMFeatureExtractor.xml @ 10:63fea23042c4 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:01:06 +0000
parents 047020d9012f
children c68cd6e1d3dc
comparison
equal deleted inserted replaced
9:047020d9012f 10:63fea23042c4
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="@TOOL_VERSION@+galaxy2" profile="20.05"> 4 <tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
16 #import re 14 #import re
17 15
18 ## Preprocessing 16 ## Preprocessing
19 mkdir in && 17 mkdir in_cond.in &&
20 #if $in 18 #if $in_cond.in_select == "no"
21 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
22 #else if $in_single 20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
23 ln -s '$in_single' 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' && 21 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
24 #end if 23 #end if
25 mkdir out && 24 mkdir out &&
26 25
27 ## Main program call 26 ## Main program call
28 27
29 set -o pipefail && 28 set -o pipefail &&
30 @EXECUTABLE@ -write_ctd ./ && 29 @EXECUTABLE@ -write_ctd ./ &&
31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
33 -in 32 -in
34 #if $in 33 #if $in_cond.in_select == "no"
35 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 34 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
36 #else if $in_single 35 #else
37 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' 36 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
38 #end if 37 #end if
39 -out 38 -out
40 'out/output.${out_type}' 39 'out/output.${out_type}'
41 40
42 ## Postprocessing 41 ## Postprocessing
47 <configfiles> 46 <configfiles>
48 <inputs name="args_json" data_style="paths"/> 47 <inputs name="args_json" data_style="paths"/>
49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 48 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
50 </configfiles> 49 </configfiles>
51 <inputs> 50 <inputs>
52 <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of -in or -in_list is required)"/> 51 <conditional name="in_cond">
53 <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s) for joint processing" help="(exactly one of -in or -in_list is required)"/> 52 <param name="in_select" type="select" label="Run tool in batch mode for -in">
54 <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=""> 53 <option value="no">No: process all datasets jointly</option>
54 <option value="yes">Yes: process each dataset in an independent job</option>
55 </param>
56 <when value="no">
57 <param argument="-in" type="data" format="idxml,mzid" multiple="true" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
58 </when>
59 <when value="yes">
60 <param argument="-in" type="data" format="idxml,mzid" multiple="false" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
61 </when>
62 </conditional>
63 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
55 <option value="idXML">idxml</option> 64 <option value="idXML">idxml</option>
56 <option value="mzid">mzid</option> 65 <option value="mzid">mzid</option>
57 <expand macro="list_string_san"/> 66 <expand macro="list_string_san" name="out_type"/>
58 </param> 67 </param>
59 <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)"> 68 <param 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)">
60 <expand macro="list_string_val"/> 69 <expand macro="list_string_val" name="extra"/>
61 <expand macro="list_string_san"/> 70 <expand macro="list_string_san" name="extra"/>
62 </param> 71 </param>
63 <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=""/> 72 <param 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=""/>
64 <expand macro="adv_opts_macro"> 73 <expand macro="adv_opts_macro">
65 <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"/> 74 <param 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"/>
66 <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"/> 75 <param 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"/>
67 <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"/> 76 <param 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"/>
68 <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"/> 77 <param 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"/>
69 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 78 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
70 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 79 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
71 <expand macro="list_string_san"/> 80 <expand macro="list_string_san" name="test"/>
72 </param> 81 </param>
73 </expand> 82 </expand>
74 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 83 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
75 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 84 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
76 </param> 85 </param>
77 </inputs> 86 </inputs>
78 <outputs> 87 <outputs>
79 <data name="out" label="${tool.name} on ${on_string}: out"> 88 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
80 <change_format> 89 <change_format>
81 <when input="out_type" value="idXML" format="idxml"/>
82 <when input="out_type" value="mzid" format="mzid"/> 90 <when input="out_type" value="mzid" format="mzid"/>
83 </change_format> 91 </change_format>
84 </data> 92 </data>
85 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 93 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
86 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 94 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
87 </data> 95 </data>
88 </outputs> 96 </outputs>
89 <tests> 97 <tests><test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
90 <expand macro="autotest_PSMFeatureExtractor"/> 98 <param name="adv_opts|test" value="true"/>
91 <expand macro="manutest_PSMFeatureExtractor"/> 99 <param name="adv_opts|skip_db_check" value="true"/>
92 </tests> 100 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
101 <param name="multiple_search_engines" value="true"/>
102 <param name="out_type" value="idxml"/>
103 <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/>
104 </test>
105 <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
106 <param name="adv_opts|test" value="true"/>
107 <param name="adv_opts|skip_db_check" value="true"/>
108 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
109 <param name="multiple_search_engines" value="true"/>
110 <param name="out_type" value="mzid"/>
111 <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>
112 </test>
113 <!-- test for the batch conditional crated for data parameters with multiple="true" -->
114 <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
115 <param name="adv_opts|test" value="true"/>
116 <param name="in_select" value="yes"/>
117 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
118 <param name="out_type" value="idxml"/>
119 <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/>
120 </test>
121 </tests>
93 <help><![CDATA[Computes extra features for each input PSM. 122 <help><![CDATA[Computes extra features for each input PSM.
94 123
95 124
96 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_PSMFeatureExtractor.html]]></help> 125 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_PSMFeatureExtractor.html]]></help>
97 <expand macro="references"/> 126 <expand macro="references"/>
98 </tool> 127 </tool>