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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 19:03:12 +0000
parents 27ddea86fe90
children
comparison
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11:76adea1e0fde 12:4d189842ebfc
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="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Interface to the SEARCH Mode of the SpectraST executable</description> 5 <description>Interface to the SEARCH Mode of the SpectraST executable</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SpectraSTSearchAdapter</token> 7 <token name="@EXECUTABLE@">SpectraSTSearchAdapter</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 spectra_files && 17 mkdir spectra_files_cond.spectra_files &&
20 ${ ' '.join(["ln -s '%s' 'spectra_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _]) } 18 #if $spectra_files_cond.spectra_files_select == "no"
19 mkdir ${' '.join(["'spectra_files_cond.spectra_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} &&
20 ${' '.join(["ln -s '%s' 'spectra_files_cond.spectra_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
21 #else
22 ln -s '$spectra_files_cond.spectra_files' 'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)' &&
23 #end if
21 mkdir output_files && 24 mkdir output_files &&
25 mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} &&
22 mkdir library_file && 26 mkdir library_file &&
23 ln -s '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' && 27 ln -s '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' &&
24 #if $sequence_database_file: 28 #if $sequence_database_file:
25 mkdir sequence_database_file && 29 mkdir sequence_database_file &&
26 ln -s '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' && 30 ln -s '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' &&
27 #end if 31 #end if
28 #if $search_file: 32 #if $search_file:
29 mkdir search_file && 33 mkdir search_file &&
30 ln -s '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' && 34 ln -s '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' &&
31 #end if 35 #end if
32 #if $adv_opts_cond.adv_opts_selector=='advanced': 36 #if $adv_opts.user_mod_file:
33 #if $adv_opts_cond.user_mod_file: 37 mkdir adv_opts.user_mod_file &&
34 mkdir adv_opts_cond.user_mod_file && 38 ln -s '$adv_opts.user_mod_file' 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' &&
35 ln -s '$adv_opts_cond.user_mod_file' 'adv_opts_cond.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts_cond.user_mod_file.ext)' &&
36 #end if 39 #end if
37 #end if
38 40
39 ## Main program call 41 ## Main program call
40 42
41 set -o pipefail && 43 set -o pipefail &&
42 @EXECUTABLE@ -write_ctd ./ && 44 @EXECUTABLE@ -write_ctd ./ &&
43 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 45 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
44 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 46 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
45 -spectra_files 47 -spectra_files
46 ${' '.join(["'spectra_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _])} 48 #if $spectra_files_cond.spectra_files_select == "no"
49 ${' '.join(["'spectra_files_cond.spectra_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
50 #else
51 'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)'
52 #end if
47 -output_files 53 -output_files
48 ${' '.join(["'output_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $output_files_type) for _ in $spectra_files if _])} 54 ${' '.join(["'output_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $output_files_type) for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
49 -library_file 55 -library_file
50 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' 56 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)'
51 #if $sequence_database_file: 57 #if $sequence_database_file:
52 -sequence_database_file 58 -sequence_database_file
53 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' 59 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)'
54 #end if 60 #end if
55 #if $search_file: 61 #if $search_file:
56 -search_file 62 -search_file
57 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' 63 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)'
58 #end if 64 #end if
59 #if $adv_opts_cond.adv_opts_selector=='advanced': 65 #if $adv_opts.user_mod_file:
60 #if $adv_opts_cond.user_mod_file:
61 -user_mod_file 66 -user_mod_file
62 'adv_opts_cond.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts_cond.user_mod_file.ext)' 67 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)'
63 #end if 68 #end if
64 #end if
65 69
66 ## Postprocessing 70 ## Postprocessing
67 ${' '.join(["&& mv -n 'output_files/%(id)s.%(omsext)s' 'output_files/%(id)s.%(gext)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "omsext":$output_files_type, "gext": $oms2gxyext(str($output_files_type))} for _ in $spectra_files if _])} 71 ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(omsext)s' 'output_files/%(bn)s/%(id)s.%(gext)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "omsext":$output_files_type, "gext": $oms2gxyext(str($output_files_type))} for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
68 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 72 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
69 && mv '@EXECUTABLE@.ctd' '$ctd_out' 73 && mv '@EXECUTABLE@.ctd' '$ctd_out'
70 #end if]]></command> 74 #end if]]></command>
71 <configfiles> 75 <configfiles>
72 <inputs name="args_json" data_style="paths"/> 76 <inputs name="args_json" data_style="paths"/>
73 <configfile name="hardcoded_json"><![CDATA[{"executable": "spectrast", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 77 <configfile name="hardcoded_json"><![CDATA[{"executable": "spectrast", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
74 </configfiles> 78 </configfiles>
75 <inputs> 79 <inputs>
76 <param name="spectra_files" argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/> 80 <conditional name="spectra_files_cond">
81 <param name="spectra_files_select" type="select" label="Run tool in batch mode for -spectra_files">
82 <option value="no">No: process all datasets jointly</option>
83 <option value="yes">Yes: process each dataset in an independent job</option>
84 </param>
85 <when value="no">
86 <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
87 </when>
88 <when value="yes">
89 <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="false" optional="false" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
90 </when>
91 </conditional>
77 <param name="output_files_type" type="select" optional="false" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)"> 92 <param name="output_files_type" type="select" optional="false" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)">
78 <option value="txt">txt</option> 93 <option value="txt">txt</option>
79 <option value="tsv">tabular (tsv)</option> 94 <option value="tsv">tabular (tsv)</option>
80 <option value="pep.xml">pepxml (pep.xml)</option> 95 <option value="pep.xml">pepxml (pep.xml)</option>
81 <option value="pepXML">pepxml</option> 96 <option value="pepXML">pepxml</option>
82 <option value="html">html</option> 97 <option value="html">html</option>
83 </param> 98 </param>
84 <param name="library_file" argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/> 99 <param argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/>
85 <param name="sequence_database_file" argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/> 100 <param argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/>
86 <param name="sequence_database_type" argument="-sequence_database_type" display="radio" type="select" optional="false" label="Specify type of sequence database" help=""> 101 <param argument="-sequence_database_type" type="select" optional="true" label="Specify type of sequence database" help="">
87 <option value="DNA">DNA</option> 102 <option value="DNA">DNA</option>
88 <option value="AA" selected="true">AA</option> 103 <option value="AA" selected="true">AA</option>
89 <expand macro="list_string_san"/> 104 <expand macro="list_string_san" name="sequence_database_type"/>
90 </param> 105 </param>
91 <param name="search_file" argument="-search_file" type="data" format="txt" optional="true" label="Only search a subset of the query spectra in the search file" help=" select txt data sets(s)"/> 106 <param argument="-search_file" type="data" format="txt" optional="true" label="Only search a subset of the query spectra in the search file" help=" select txt data sets(s)"/>
92 <param name="precursor_mz_tolerance" argument="-precursor_mz_tolerance" type="float" optional="true" min="0.0" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="Monoisotopic mass is assumed"/> 107 <param argument="-precursor_mz_tolerance" type="float" optional="true" min="0.0" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="Monoisotopic mass is assumed"/>
93 <expand macro="adv_opts_macro"> 108 <expand macro="adv_opts_macro">
94 <param name="use_isotopically_averaged_mass" argument="-use_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/> 109 <param argument="-use_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/>
95 <param name="use_all_charge_states" argument="-use_all_charge_states" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search library spectra of all charge states" help="i.e., ignore specified charge state (if any) of the query spectrum"/> 110 <param argument="-use_all_charge_states" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search library spectra of all charge states" help="i.e., ignore specified charge state (if any) of the query spectrum"/>
96 <param name="user_mod_file" argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is &quot;spectrast.usermods&quot; select txt data sets(s)"/> 111 <param argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is &quot;spectrast.usermods&quot; select txt data sets(s)"/>
97 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 112 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
98 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 113 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
99 <expand macro="list_string_san"/> 114 <expand macro="list_string_san" name="test"/>
100 </param> 115 </param>
101 </expand> 116 </expand>
102 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 117 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
103 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 118 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
104 </param> 119 </param>
105 </inputs> 120 </inputs>
106 <outputs> 121 <outputs>
107 <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files"> 122 <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">
108 <discover_datasets directory="output_files" pattern="__name_and_ext__"/> 123 <discover_datasets directory="output_files" recurse="true" pattern="__name_and_ext__"/>
109 </collection> 124 </collection>
110 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 125 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
111 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 126 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
112 </data> 127 </data>
113 </outputs> 128 </outputs>
114 <tests> 129 <tests><!-- TOPP_SpectrastSearchAdapter_1 -->
115 <expand macro="autotest_SpectraSTSearchAdapter"/> 130 <!-- TOPP_SpectrastSearchAdapter_2 -->
116 <expand macro="manutest_SpectraSTSearchAdapter"/>
117 </tests> 131 </tests>
118 <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable 132 <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable
119 133
120 134
121 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SpectraSTSearchAdapter.html]]></help> 135 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SpectraSTSearchAdapter.html]]></help>
122 <expand macro="references"/> 136 <expand macro="references"/>
123 </tool> 137 </tool>