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comparison SpectraSTSearchAdapter.xml @ 13:52dd59548339 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:34:58 +0000
parents 4d189842ebfc
children
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12:4d189842ebfc 13:52dd59548339
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 &quot;spectrast.usermods&quot; 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 &quot;spectrast.usermods&quot; 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>