Mercurial > repos > galaxyp > openms_spectrastsearchadapter

annotate SpectraSTSearchAdapter.xml @ 12:4d189842ebfc 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 19:03:12 +0000
parents 27ddea86fe90
children 52dd59548339
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Interface to the SEARCH Mode of the SpectraST executable</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SpectraSTSearchAdapter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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16 ## Preprocessing
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17 mkdir spectra_files_cond.spectra_files &&
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18 #if $spectra_files_cond.spectra_files_select == "no"
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19 mkdir ${' '.join(["'spectra_files_cond.spectra_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} &&
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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])}
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21 #else
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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)' &&
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23 #end if
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24 mkdir output_files &&
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25 mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} &&
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26 mkdir library_file &&
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27 ln -s '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' &&
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28 #if $sequence_database_file:
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29 mkdir sequence_database_file &&
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30 ln -s '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' &&
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31 #end if
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32 #if $search_file:
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33 mkdir search_file &&
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34 ln -s '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' &&
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35 #end if
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36 #if $adv_opts.user_mod_file:
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37 mkdir adv_opts.user_mod_file &&
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38 ln -s '$adv_opts.user_mod_file' 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' &&
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39 #end if
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41 ## Main program call
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43 set -o pipefail &&
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44 @EXECUTABLE@ -write_ctd ./ &&
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45 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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46 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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47 -spectra_files
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48 #if $spectra_files_cond.spectra_files_select == "no"
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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])}
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50 #else
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51 'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)'
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52 #end if
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53 -output_files
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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])}
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55 -library_file
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56 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)'
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57 #if $sequence_database_file:
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58 -sequence_database_file
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59 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)'
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60 #end if
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61 #if $search_file:
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62 -search_file
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63 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)'
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64 #end if
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65 #if $adv_opts.user_mod_file:
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66 -user_mod_file
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67 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)'
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68 #end if
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69
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70 ## Postprocessing
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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])}
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72 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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73 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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74 #end if]]></command>
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75 <configfiles>
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76 <inputs name="args_json" data_style="paths"/>
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77 <configfile name="hardcoded_json"><![CDATA[{"executable": "spectrast", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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78 </configfiles>
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79 <inputs>
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80 <conditional name="spectra_files_cond">
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81 <param name="spectra_files_select" type="select" label="Run tool in batch mode for -spectra_files">
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82 <option value="no">No: process all datasets jointly</option>
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83 <option value="yes">Yes: process each dataset in an independent job</option>
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84 </param>
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85 <when value="no">
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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)"/>
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87 </when>
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88 <when value="yes">
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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)"/>
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90 </when>
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91 </conditional>
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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)">
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93 <option value="txt">txt</option>
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94 <option value="tsv">tabular (tsv)</option>
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95 <option value="pep.xml">pepxml (pep.xml)</option>
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96 <option value="pepXML">pepxml</option>
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97 <option value="html">html</option>
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98 </param>
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99 <param argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/>
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100 <param argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/>
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101 <param argument="-sequence_database_type" type="select" optional="true" label="Specify type of sequence database" help="">
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102 <option value="DNA">DNA</option>
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103 <option value="AA" selected="true">AA</option>
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104 <expand macro="list_string_san" name="sequence_database_type"/>
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105 </param>
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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)"/>
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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"/>
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108 <expand macro="adv_opts_macro">
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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=""/>
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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"/>
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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)"/>
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112 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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113 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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114 <expand macro="list_string_san" name="test"/>
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115 </param>
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116 </expand>
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117 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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118 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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119 </param>
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120 </inputs>
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121 <outputs>
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122 <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">
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123 <discover_datasets directory="output_files" recurse="true" pattern="__name_and_ext__"/>
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124 </collection>
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125 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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126 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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127 </data>
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128 </outputs>
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129 <tests><!-- TOPP_SpectrastSearchAdapter_1 -->
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130 <!-- TOPP_SpectrastSearchAdapter_2 -->
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131 </tests>
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132 <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable
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133
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134
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135 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SpectraSTSearchAdapter.html]]></help>
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136 <expand macro="references"/>
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137 </tool>