Mercurial > repos > galaxyp > openms_spectrastsearchadapter

comparison SpectraSTSearchAdapter.xml @ 8:28e96ae21a44 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:53:13 +0000
parents ab22e4296eaf
children 27ddea86fe90
comparison
equal deleted inserted replaced
7:df3f606e184d 8:28e96ae21a44
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="2.3.0"> 4 <tool id="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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>
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[SpectraSTSearchAdapter 15 @EXT_FOO@
16 #import re
14 17
15 -spectra_files 18 ## Preprocessing
16 #for token in $param_spectra_files: 19 mkdir spectra_files &&
17 $token 20 ${ ' '.join(["ln -s '%s' 'spectra_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _]) }
18 #end for 21 mkdir output_files &&
19 22 mkdir library_file &&
20 #if $rep_param_output_files: 23 ln -s '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' &&
21 -output_files 24 #if $sequence_database_file:
22 #for token in $rep_param_output_files: 25 mkdir sequence_database_file &&
23 #if " " in str(token): 26 ln -s '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' &&
24 "$token.param_output_files"
25 #else
26 $token.param_output_files
27 #end if
28 #end for
29 #end if 27 #end if
30 #if $param_library_file: 28 #if $search_file:
31 -library_file $param_library_file 29 mkdir search_file &&
30 ln -s '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' &&
32 #end if 31 #end if
33 #if $param_sequence_database_file: 32 #if $adv_opts_cond.adv_opts_selector=='advanced':
34 -sequence_database_file $param_sequence_database_file 33 #if $adv_opts_cond.user_mod_file:
35 #end if 34 mkdir adv_opts_cond.user_mod_file &&
36 #if $param_sequence_database_type: 35 ln -s '$adv_opts_cond.user_mod_file' 'adv_opts_cond.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts_cond.user_mod_file.ext)' &&
37 -sequence_database_type
38 #if " " in str($param_sequence_database_type):
39 "$param_sequence_database_type"
40 #else
41 $param_sequence_database_type
42 #end if 36 #end if
43 #end if 37 #end if
44 #if $param_search_file: 38
45 -search_file $param_search_file 39 ## Main program call
40
41 set -o pipefail &&
42 @EXECUTABLE@ -write_ctd ./ &&
43 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
44 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
45 -spectra_files
46 ${' '.join(["'spectra_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _])}
47 -output_files
48 ${' '.join(["'output_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $output_files_type) for _ in $spectra_files if _])}
49 -library_file
50 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)'
51 #if $sequence_database_file:
52 -sequence_database_file
53 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)'
46 #end if 54 #end if
47 #if $param_params_file: 55 #if $search_file:
48 -params_file $param_params_file 56 -search_file
57 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)'
49 #end if 58 #end if
50 #if $param_precursor_mz_tolerance: 59 #if $adv_opts_cond.adv_opts_selector=='advanced':
51 -precursor_mz_tolerance $param_precursor_mz_tolerance 60 #if $adv_opts_cond.user_mod_file:
61 -user_mod_file
62 'adv_opts_cond.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts_cond.user_mod_file.ext)'
63 #end if
52 #end if 64 #end if
53 #if $adv_opts.adv_opts_selector=='advanced': 65
54 #if $adv_opts.param_use_isotopically_averaged_mass: 66 ## Postprocessing
55 -use_isotopically_averaged_mass 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 _])}
56 #end if 68 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
57 #if $adv_opts.param_use_all_charge_states: 69 && mv '@EXECUTABLE@.ctd' '$ctd_out'
58 -use_all_charge_states 70 #end if]]></command>
59 #end if 71 <configfiles>
60 #if $adv_opts.param_user_mod_file: 72 <inputs name="args_json" data_style="paths"/>
61 -user_mod_file $adv_opts.param_user_mod_file 73 <configfile name="hardcoded_json"><![CDATA[{"executable": "spectrast", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
62 #end if 74 </configfiles>
63 #if $adv_opts.param_force:
64 -force
65 #end if
66 #end if
67 ]]></command>
68 <inputs> 75 <inputs>
69 <param name="param_spectra_files" type="data" format="mzml,mzxml,mzData,dta,msp" multiple="true" optional="False" size="30" label="File names(s) of spectra to be searched" help="(-spectra_files) "> 76 <param name="spectra_files" argument="-spectra_files" type="data" format="dta,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,msp,mzdata,mzml,mzxml data sets(s)"/>
70 <sanitizer> 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)">
71 <valid initial="string.printable"> 78 <option value="txt">txt</option>
72 <remove value="'"/> 79 <option value="tsv">tabular (tsv)</option>
73 <remove value="&quot;"/> 80 <option value="pep.xml">pepxml (pep.xml)</option>
74 </valid> 81 <option value="xml">xml</option>
75 </sanitizer> 82 <option value="pepXML">pepxml</option>
83 <option value="html">html</option>
76 </param> 84 </param>
77 <param name="param_library_file" type="data" format="splib" optional="False" label="Specify library file" help="(-library_file) "/> 85 <param name="library_file" argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/>
78 <param name="param_sequence_database_file" type="data" format="fasta" optional="True" label="The sequence database" help="(-sequence_database_file) "/> 86 <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)"/>
79 <param name="param_sequence_database_type" display="radio" type="select" optional="False" value="AA" label="Specify type of sequence database" help="(-sequence_database_type) "> 87 <param name="sequence_database_type" argument="-sequence_database_type" display="radio" type="select" optional="false" label="Specify type of sequence database" help="">
80 <option value="DNA">DNA</option> 88 <option value="DNA">DNA</option>
81 <option value="AA" selected="true">AA</option> 89 <option value="AA" selected="true">AA</option>
90 <expand macro="list_string_san"/>
82 </param> 91 </param>
83 <param name="param_search_file" type="data" format="txt,dat" optional="True" label="Only search a subset of the query spectra in the search file" help="(-search_file) "/> 92 <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)"/>
84 <param name="param_params_file" type="data" format="params" optional="True" label="Read search options from file" help="(-params_file) All options set in the file will be overridden by command-line options, if specified"/> 93 <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"/>
85 <param name="param_precursor_mz_tolerance" type="float" min="0.0" optional="True" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="(-precursor_mz_tolerance) Monoisotopic mass is assumed"/> 94 <expand macro="adv_opts_macro">
86 <expand macro="advanced_options"> 95 <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=""/>
87 <param name="param_use_isotopically_averaged_mass" display="radio" type="boolean" truevalue="-use_isotopically_averaged_mass" falsevalue="" checked="false" optional="True" label="Use isotopically averaged mass instead of monoisotopic mass" help="(-use_isotopically_averaged_mass) "/> 96 <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"/>
88 <param name="param_use_all_charge_states" display="radio" type="boolean" truevalue="-use_all_charge_states" falsevalue="" checked="false" optional="True" label="Search library spectra of all charge states, i.e., ignore specified charge state (if any) of the query spectrum" help="(-use_all_charge_states) "/> 97 <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)"/>
89 <param name="param_user_mod_file" type="data" format="txt" label="Specify name of user-defined modifications file" help="(-user_mod_file) Default is &quot;spectrast.usermods&quot;"/> 98 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 99 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
100 <expand macro="list_string_san"/>
101 </param>
91 </expand> 102 </expand>
103 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
104 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
105 </param>
92 </inputs> 106 </inputs>
93 <outputs> 107 <outputs>
94 <data name="param_output_files" format="txt"/> 108 <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">
109 <discover_datasets directory="output_files" pattern="__name_and_ext__"/>
110 </collection>
111 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
112 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
113 </data>
95 </outputs> 114 </outputs>
96 <help>Interface to the SEARCH Mode of the SpectraST executable 115 <tests>
116 <expand macro="autotest_SpectraSTSearchAdapter"/>
117 <expand macro="manutest_SpectraSTSearchAdapter"/>
118 </tests>
119 <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable
97 120
98 121
99 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SpectraSTSearchAdapter.html</help> 122 For more information, visit http://www.openms.de/documentation/UTILS_SpectraSTSearchAdapter.html]]></help>
123 <expand macro="references"/>
100 </tool> 124 </tool>