Mercurial > repos > galaxyp > openms_gnpsexport
comparison GNPSExport.xml @ 4:2da14ae3844a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 18:57:27 +0000 |
parents | 2dabae2814df |
children | 87a970d1514b |
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3:d5cb5af21850 | 4:2da14ae3844a |
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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: []--> | 3 <!--Proposed Tool Section: [File Handling]--> |
4 <tool id="GNPSExport" name="GNPSExport" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="GNPSExport" name="GNPSExport" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Tool to export consensus features into MGF format</description> | 5 <description>Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format. |
6 See the documentation on https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-openms</description> | |
6 <macros> | 7 <macros> |
7 <token name="@EXECUTABLE@">GNPSExport</token> | 8 <token name="@EXECUTABLE@">GNPSExport</token> |
8 <import>macros.xml</import> | 9 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
11 </macros> | 10 </macros> |
12 <expand macro="requirements"/> | 11 <expand macro="requirements"/> |
13 <expand macro="stdio"/> | 12 <expand macro="stdio"/> |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | 13 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
15 @EXT_FOO@ | 14 @EXT_FOO@ |
16 #import re | 15 #import re |
17 | 16 |
18 ## Preprocessing | 17 ## Preprocessing |
19 mkdir in_cm && | 18 mkdir in_cm && |
20 ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' && | 19 ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' && |
21 mkdir in_mzml && | 20 mkdir in_mzml_cond.in_mzml && |
22 ${ ' '.join(["ln -s '%s' 'in_mzml/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_mzml if _]) } | 21 #if $in_mzml_cond.in_mzml_select == "no" |
22 mkdir ${' '.join(["'in_mzml_cond.in_mzml/%s'" % (i) for i, f in enumerate($in_mzml_cond.in_mzml) if f])} && | |
23 ${' '.join(["ln -s '%s' 'in_mzml_cond.in_mzml/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_mzml_cond.in_mzml) if f])} | |
24 #else | |
25 ln -s '$in_mzml_cond.in_mzml' 'in_mzml_cond.in_mzml/${re.sub("[^\w\-_]", "_", $in_mzml_cond.in_mzml.element_identifier)}.$gxy2omsext($in_mzml_cond.in_mzml.ext)' && | |
26 #end if | |
23 mkdir out && | 27 mkdir out && |
24 | 28 |
25 ## Main program call | 29 ## Main program call |
26 | 30 |
27 set -o pipefail && | 31 set -o pipefail && |
29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | 33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | 34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
31 -in_cm | 35 -in_cm |
32 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' | 36 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' |
33 -in_mzml | 37 -in_mzml |
34 ${' '.join(["'in_mzml/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_mzml if _])} | 38 #if $in_mzml_cond.in_mzml_select == "no" |
39 ${' '.join(["'in_mzml_cond.in_mzml/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_mzml_cond.in_mzml) if f])} | |
40 #else | |
41 'in_mzml_cond.in_mzml/${re.sub("[^\w\-_]", "_", $in_mzml_cond.in_mzml.element_identifier)}.$gxy2omsext($in_mzml_cond.in_mzml.ext)' | |
42 #end if | |
35 -out | 43 -out |
36 'out/output.${gxy2omsext("mgf")}' | 44 'out/output.${gxy2omsext("mgf")}' |
37 | 45 |
38 ## Postprocessing | 46 ## Postprocessing |
39 && mv 'out/output.${gxy2omsext("mgf")}' '$out' | 47 && mv 'out/output.${gxy2omsext("mgf")}' '$out' |
43 <configfiles> | 51 <configfiles> |
44 <inputs name="args_json" data_style="paths"/> | 52 <inputs name="args_json" data_style="paths"/> |
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
46 </configfiles> | 54 </configfiles> |
47 <inputs> | 55 <inputs> |
48 <param name="in_cm" argument="-in_cm" type="data" format="consensusxml" optional="false" label="input file containing consensus elements with 'peptide' annotations" help=" select consensusxml data sets(s)"/> | 56 <param argument="-in_cm" type="data" format="consensusxml" optional="false" label="Input consensusXML file containing only consensusElements with "peptide" annotations" help=" select consensusxml data sets(s)"/> |
49 <param name="in_mzml" argument="-in_mzml" type="data" format="mzml" multiple="true" optional="false" label="original mzml files containing ms/ms spectrum information" help=" select mzml data sets(s)"/> | 57 <conditional name="in_mzml_cond"> |
50 <param name="output_type" argument="-output_type" display="radio" type="select" optional="false" label="specificity of mgf output information" help=""> | 58 <param name="in_mzml_select" type="select" label="Run tool in batch mode for -in_mzml"> |
51 <option value="full_spectra" selected="true">full_spectra</option> | 59 <option value="no">No: process all datasets jointly</option> |
60 <option value="yes">Yes: process each dataset in an independent job</option> | |
61 </param> | |
62 <when value="no"> | |
63 <param argument="-in_mzml" type="data" format="mzml" multiple="true" optional="false" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/> | |
64 </when> | |
65 <when value="yes"> | |
66 <param argument="-in_mzml" type="data" format="mzml" multiple="false" optional="false" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/> | |
67 </when> | |
68 </conditional> | |
69 <param argument="-output_type" type="select" optional="true" label="specificity of mgf output information" help=""> | |
52 <option value="merged_spectra">merged_spectra</option> | 70 <option value="merged_spectra">merged_spectra</option> |
53 <expand macro="list_string_san"/> | 71 <option value="most_intense" selected="true">most_intense</option> |
72 <expand macro="list_string_san" name="output_type"/> | |
54 </param> | 73 </param> |
55 <param name="precursor_mz_tolerance" argument="-precursor_mz_tolerance" type="float" optional="true" value="0.0001" label="Tolerance mz window for precursor selection" help=""/> | 74 <param argument="-peptide_cutoff" type="integer" optional="true" min="-1" value="5" label="Number of most intense peptides to consider per consensus element; '-1' to consider all identifications" help=""/> |
56 <param name="precursor_rt_tolerance" argument="-precursor_rt_tolerance" type="float" optional="true" value="5.0" label="Tolerance rt window for precursor selection" help=""/> | 75 <param argument="-ms2_bin_size" type="float" optional="true" min="0.0" value="0.019999999552965" label="Bin size (Da) for fragment ions when merging ms2 scans" help=""/> |
57 <section name="merged_spectra" title="Options for exporting mgf file with merged spectra per feature" help="" expanded="false"> | 76 <section name="merged_spectra" title="Options for exporting mgf file with merged spectra per consensusElement" help="" expanded="false"> |
58 <param name="cos_similarity" argument="-merged_spectra:cos_similarity" type="float" optional="true" value="0.95" label="Cosine similarity threshold for merged_spectra output" help=""/> | 77 <param name="cos_similarity" argument="-merged_spectra:cos_similarity" type="float" optional="true" min="0.0" value="0.9" label="Cosine similarity threshold for merged_spectra output" help=""/> |
59 </section> | 78 </section> |
60 <expand macro="adv_opts_macro"> | 79 <expand macro="adv_opts_macro"> |
61 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 80 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
62 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 81 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
63 <expand macro="list_string_san"/> | 82 <expand macro="list_string_san" name="test"/> |
64 </param> | 83 </param> |
65 </expand> | 84 </expand> |
66 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 85 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
67 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 86 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
68 </param> | 87 </param> |
71 <data name="out" label="${tool.name} on ${on_string}: out" format="mgf"/> | 90 <data name="out" label="${tool.name} on ${on_string}: out" format="mgf"/> |
72 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 91 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
73 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 92 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
74 </data> | 93 </data> |
75 </outputs> | 94 </outputs> |
76 <tests> | 95 <tests><!-- TOPP_GNPSExport_1 --> |
77 <expand macro="autotest_GNPSExport"/> | 96 <test expect_num_outputs="2"> |
78 <expand macro="manutest_GNPSExport"/> | 97 <section name="adv_opts"> |
98 <param name="force" value="false"/> | |
99 <param name="test" value="true"/> | |
100 </section> | |
101 <param name="in_cm" value="GNPSExport_cons1.consensusXML"/> | |
102 <conditional name="in_mzml_cond"> | |
103 <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/> | |
104 </conditional> | |
105 <output name="out" file="GNPSExport_1_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/> | |
106 <param name="output_type" value="most_intense"/> | |
107 <param name="peptide_cutoff" value="10"/> | |
108 <param name="ms2_bin_size" value="2.0"/> | |
109 <section name="merged_spectra"> | |
110 <param name="cos_similarity" value="0.85"/> | |
111 </section> | |
112 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
113 <output name="ctd_out" ftype="xml"> | |
114 <assert_contents> | |
115 <is_valid_xml/> | |
116 </assert_contents> | |
117 </output> | |
118 </test> | |
119 <!-- TOPP_GNPSExport_2 --> | |
120 <test expect_num_outputs="2"> | |
121 <section name="adv_opts"> | |
122 <param name="force" value="false"/> | |
123 <param name="test" value="true"/> | |
124 </section> | |
125 <param name="in_cm" value="GNPSExport_cons1.consensusXML"/> | |
126 <conditional name="in_mzml_cond"> | |
127 <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/> | |
128 </conditional> | |
129 <output name="out" file="GNPSExport_2_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/> | |
130 <param name="output_type" value="merged_spectra"/> | |
131 <param name="peptide_cutoff" value="10"/> | |
132 <param name="ms2_bin_size" value="2.0"/> | |
133 <section name="merged_spectra"> | |
134 <param name="cos_similarity" value="0.85"/> | |
135 </section> | |
136 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
137 <output name="ctd_out" ftype="xml"> | |
138 <assert_contents> | |
139 <is_valid_xml/> | |
140 </assert_contents> | |
141 </output> | |
142 </test> | |
143 <!-- TOPP_GNPSExport_3 --> | |
144 <test expect_num_outputs="2"> | |
145 <section name="adv_opts"> | |
146 <param name="force" value="false"/> | |
147 <param name="test" value="true"/> | |
148 </section> | |
149 <param name="in_cm" value="GNPSExport_cons1.consensusXML"/> | |
150 <conditional name="in_mzml_cond"> | |
151 <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/> | |
152 </conditional> | |
153 <output name="out" file="GNPSExport_3_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/> | |
154 <param name="output_type" value="most_intense"/> | |
155 <param name="peptide_cutoff" value="10"/> | |
156 <param name="ms2_bin_size" value="0.02"/> | |
157 <section name="merged_spectra"> | |
158 <param name="cos_similarity" value="0.85"/> | |
159 </section> | |
160 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
161 <output name="ctd_out" ftype="xml"> | |
162 <assert_contents> | |
163 <is_valid_xml/> | |
164 </assert_contents> | |
165 </output> | |
166 </test> | |
79 </tests> | 167 </tests> |
80 <help><![CDATA[Tool to export consensus features into MGF format | 168 <help><![CDATA[Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format. |
169 See the documentation on https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-openms | |
81 | 170 |
82 ]]></help> | 171 |
172 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_GNPSExport.html]]></help> | |
83 <expand macro="references"/> | 173 <expand macro="references"/> |
84 </tool> | 174 </tool> |