Mercurial > repos > galaxyp > openms_spectrastsearchadapter
comparison SpectraSTSearchAdapter.xml @ 13:52dd59548339 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
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date | Fri, 14 Jun 2024 21:34:58 +0000 |
parents | 4d189842ebfc |
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12:4d189842ebfc | 13:52dd59548339 |
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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.--> | 1 <!--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]--> | 2 <!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]--> |
4 <tool id="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | 3 <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> | 4 <description>Interface to the SEARCH Mode of the SpectraST executable</description> |
6 <macros> | 5 <macros> |
7 <token name="@EXECUTABLE@">SpectraSTSearchAdapter</token> | 6 <token name="@EXECUTABLE@">SpectraSTSearchAdapter</token> |
8 <import>macros.xml</import> | 7 <import>macros.xml</import> |
15 | 14 |
16 ## Preprocessing | 15 ## Preprocessing |
17 mkdir spectra_files_cond.spectra_files && | 16 mkdir spectra_files_cond.spectra_files && |
18 #if $spectra_files_cond.spectra_files_select == "no" | 17 #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])} && | 18 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])} | 19 ${' '.join(["cp '%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 | 20 #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($spectra_files_cond.spectra_files.ext)' && | 21 cp '$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 | 22 #end if |
24 mkdir output_files && | 23 mkdir output_files && |
25 mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} && | 24 mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} && |
26 mkdir library_file && | 25 mkdir library_file && |
27 ln -s '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' && | 26 cp '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' && |
28 #if $sequence_database_file: | 27 #if $sequence_database_file: |
29 mkdir sequence_database_file && | 28 mkdir sequence_database_file && |
30 ln -s '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' && | 29 cp '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' && |
31 #end if | 30 #end if |
32 #if $search_file: | 31 #if $search_file: |
33 mkdir search_file && | 32 mkdir search_file && |
34 ln -s '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' && | 33 cp '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' && |
35 #end if | 34 #end if |
35 ## advanced options | |
36 #if $adv_opts.user_mod_file: | 36 #if $adv_opts.user_mod_file: |
37 mkdir adv_opts.user_mod_file && | 37 mkdir adv_opts.user_mod_file && |
38 ln -s '$adv_opts.user_mod_file' 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' && | 38 cp '$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)' && |
39 #end if | 39 #end if |
40 | |
40 | 41 |
41 ## Main program call | 42 ## Main program call |
42 | 43 |
43 set -o pipefail && | 44 set -o pipefail && |
44 @EXECUTABLE@ -write_ctd ./ && | 45 @EXECUTABLE@ -write_ctd ./ && |
60 #end if | 61 #end if |
61 #if $search_file: | 62 #if $search_file: |
62 -search_file | 63 -search_file |
63 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' | 64 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' |
64 #end if | 65 #end if |
66 ## advanced options | |
65 #if $adv_opts.user_mod_file: | 67 #if $adv_opts.user_mod_file: |
66 -user_mod_file | 68 -user_mod_file |
67 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' | 69 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' |
68 #end if | 70 #end if |
71 | |
69 | 72 |
70 ## Postprocessing | 73 ## Postprocessing |
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])} | 74 ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(omsext)s' 'output_files/%(bn)s/%(id)s.%(gext)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "omsext":$output_files_type, "gext": $oms2gxyext(str($output_files_type))} for i, f in enumerate($spectra_files_cond.spectra_files) if f])} |
72 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS | 75 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
73 && mv '@EXECUTABLE@.ctd' '$ctd_out' | 76 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
81 <param name="spectra_files_select" type="select" label="Run tool in batch mode for -spectra_files"> | 84 <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> | 85 <option value="no">No: process all datasets jointly</option> |
83 <option value="yes">Yes: process each dataset in an independent job</option> | 86 <option value="yes">Yes: process each dataset in an independent job</option> |
84 </param> | 87 </param> |
85 <when value="no"> | 88 <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)"/> | 89 <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="true" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/> |
87 </when> | 90 </when> |
88 <when value="yes"> | 91 <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)"/> | 92 <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/> |
90 </when> | 93 </when> |
91 </conditional> | 94 </conditional> |
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)"> | 95 <param name="output_files_type" type="select" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)"> |
93 <option value="txt">txt</option> | 96 <option value="txt">txt</option> |
94 <option value="tsv">tabular (tsv)</option> | 97 <option value="tsv">tabular (tsv)</option> |
95 <option value="pep.xml">pepxml (pep.xml)</option> | 98 <option value="pep.xml">pepxml (pep.xml)</option> |
96 <option value="pepXML">pepxml</option> | 99 <option value="pepXML">pepxml</option> |
97 <option value="html">html</option> | 100 <option value="html">html</option> |
98 </param> | 101 </param> |
99 <param argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/> | 102 <param argument="-library_file" type="data" format="splib" label="Specify library file" help=" select splib 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)"/> | 103 <param argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/> |
101 <param argument="-sequence_database_type" type="select" optional="true" label="Specify type of sequence database" help=""> | 104 <param argument="-sequence_database_type" type="select" label="Specify type of sequence database" help=""> |
102 <option value="DNA">DNA</option> | 105 <option value="DNA">DNA</option> |
103 <option value="AA" selected="true">AA</option> | 106 <option value="AA" selected="true">AA</option> |
104 <expand macro="list_string_san" name="sequence_database_type"/> | 107 <expand macro="list_string_san" name="sequence_database_type"/> |
105 </param> | 108 </param> |
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)"/> | 109 <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)"/> |
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"/> | 110 <param argument="-precursor_mz_tolerance" type="float" 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"/> |
108 <expand macro="adv_opts_macro"> | 111 <expand macro="adv_opts_macro"> |
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=""/> | 112 <param argument="-use_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/> |
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"/> | 113 <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"/> |
111 <param argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is "spectrast.usermods" select txt data sets(s)"/> | 114 <param argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is "spectrast.usermods" select txt data sets(s)"/> |
112 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 115 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
113 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 116 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> |
114 <expand macro="list_string_san" name="test"/> | 117 <expand macro="list_string_san" name="test"/> |
115 </param> | 118 </param> |
116 </expand> | 119 </expand> |
117 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 120 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
118 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 121 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
124 </collection> | 127 </collection> |
125 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 128 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
126 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 129 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
127 </data> | 130 </data> |
128 </outputs> | 131 </outputs> |
129 <tests><!-- TOPP_SpectrastSearchAdapter_1 --> | 132 <tests> |
133 <!-- TOPP_SpectrastSearchAdapter_1 --> | |
130 <!-- TOPP_SpectrastSearchAdapter_2 --> | 134 <!-- TOPP_SpectrastSearchAdapter_2 --> |
131 </tests> | 135 </tests> |
132 <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable | 136 <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable |
133 | 137 |
134 | 138 |
135 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SpectraSTSearchAdapter.html]]></help> | 139 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraSTSearchAdapter.html]]></help> |
136 <expand macro="references"/> | 140 <expand macro="references"/> |
137 </tool> | 141 </tool> |