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comparison PeptideIndexer.xml @ 13:d6aca689dd48 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 19:11:03 +0000
parents d8ee5700c66b
children 0693b186f39e
comparison
equal deleted inserted replaced
12:dd173849c3d8 13:d6aca689dd48
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: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="PeptideIndexer" name="PeptideIndexer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="PeptideIndexer" name="PeptideIndexer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Refreshes the protein references for all peptide hits.</description> 5 <description>Refreshes the protein references for all peptide hits.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PeptideIndexer</token> 7 <token name="@EXECUTABLE@">PeptideIndexer</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
47 <configfiles> 45 <configfiles>
48 <inputs name="args_json" data_style="paths"/> 46 <inputs name="args_json" data_style="paths"/>
49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
50 </configfiles> 48 </configfiles>
51 <inputs> 49 <inputs>
52 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/> 50 <param argument="-in" type="data" format="idxml" optional="false" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/>
53 <param name="fasta" argument="-fasta" type="data" format="fasta" optional="true" label="Input sequence database in FASTA format" help="Leave empty for using the same DB as used for the input idXML (this might fail). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/> 51 <param argument="-fasta" type="data" format="fasta" optional="true" label="Input sequence database in FASTA format" help="Leave empty for using the same DB as used for the input idXML (this might fail). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
54 <param name="decoy_string" argument="-decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)"> 52 <param argument="-decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
55 <expand macro="list_string_san"/> 53 <expand macro="list_string_san" name="decoy_string"/>
56 </param> 54 </param>
57 <param name="decoy_string_position" argument="-decoy_string_position" display="radio" type="select" optional="false" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)"> 55 <param argument="-decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
58 <option value="prefix" selected="true">prefix</option> 56 <option value="prefix" selected="true">prefix</option>
59 <option value="suffix">suffix</option> 57 <option value="suffix">suffix</option>
60 <expand macro="list_string_san"/> 58 <expand macro="list_string_san" name="decoy_string_position"/>
61 </param> 59 </param>
62 <param name="missing_decoy_action" argument="-missing_decoy_action" display="radio" type="select" optional="false" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help=""> 60 <param argument="-missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
63 <option value="error" selected="true">error</option> 61 <option value="error" selected="true">error</option>
64 <option value="warn">warn</option> 62 <option value="warn">warn</option>
65 <option value="silent">silent</option> 63 <option value="silent">silent</option>
66 <expand macro="list_string_san"/> 64 <expand macro="list_string_san" name="missing_decoy_action"/>
67 </param> 65 </param>
68 <param name="write_protein_sequence" argument="-write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/> 66 <param argument="-write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
69 <param name="write_protein_description" argument="-write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/> 67 <param argument="-write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
70 <param name="keep_unreferenced_proteins" argument="-keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/> 68 <param argument="-keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
71 <param name="unmatched_action" argument="-unmatched_action" display="radio" type="select" optional="false" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help=""> 69 <param argument="-unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
72 <option value="error" selected="true">error</option> 70 <option value="error" selected="true">error</option>
73 <option value="warn">warn</option> 71 <option value="warn">warn</option>
74 <option value="remove">remove</option> 72 <option value="remove">remove</option>
75 <expand macro="list_string_san"/> 73 <expand macro="list_string_san" name="unmatched_action"/>
76 </param> 74 </param>
77 <param name="aaa_max" argument="-aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are B, J, Z and X!"/> 75 <param argument="-aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
78 <param name="mismatches_max" argument="-mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/> 76 <param argument="-mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
79 <param name="IL_equivalent" argument="-IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/> 77 <param argument="-IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
80 <section name="enzyme" title="" help="" expanded="false"> 78 <section name="enzyme" title="" help="" expanded="false">
81 <param name="name" argument="-enzyme:name" type="select" optional="false" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input"> 79 <param name="name" argument="-enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
82 <option value="auto" selected="true">auto</option> 80 <option value="auto" selected="true">auto</option>
81 <option value="Arg-C">Arg-C</option>
82 <option value="Arg-C/P">Arg-C/P</option>
83 <option value="Asp-N">Asp-N</option>
83 <option value="Asp-N/B">Asp-N/B</option> 84 <option value="Asp-N/B">Asp-N/B</option>
84 <option value="Asp-N_ambic">Asp-N_ambic</option> 85 <option value="Asp-N_ambic">Asp-N_ambic</option>
85 <option value="Chymotrypsin">Chymotrypsin</option> 86 <option value="Chymotrypsin">Chymotrypsin</option>
86 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 87 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
87 <option value="CNBr">CNBr</option> 88 <option value="CNBr">CNBr</option>
89 <option value="Formic_acid">Formic_acid</option>
90 <option value="Lys-C">Lys-C</option>
91 <option value="Lys-N">Lys-N</option>
92 <option value="Trypsin/P">Trypsin/P</option>
93 <option value="V8-DE">V8-DE</option>
94 <option value="V8-E">V8-E</option>
95 <option value="leukocyte elastase">leukocyte elastase</option>
88 <option value="proline endopeptidase">proline endopeptidase</option> 96 <option value="proline endopeptidase">proline endopeptidase</option>
89 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 97 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
90 <option value="Alpha-lytic protease">Alpha-lytic protease</option> 98 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
91 <option value="2-iodobenzoate">2-iodobenzoate</option> 99 <option value="2-iodobenzoate">2-iodobenzoate</option>
92 <option value="iodosobenzoate">iodosobenzoate</option> 100 <option value="iodosobenzoate">iodosobenzoate</option>
93 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 101 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
94 <option value="PepsinA">PepsinA</option>
95 <option value="TrypChymo">TrypChymo</option>
96 <option value="Trypsin/P">Trypsin/P</option>
97 <option value="V8-DE">V8-DE</option>
98 <option value="V8-E">V8-E</option>
99 <option value="leukocyte elastase">leukocyte elastase</option>
100 <option value="Arg-C">Arg-C</option>
101 <option value="Arg-C/P">Arg-C/P</option>
102 <option value="Asp-N">Asp-N</option>
103 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 102 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
104 <option value="Glu-C+P">Glu-C+P</option> 103 <option value="Glu-C+P">Glu-C+P</option>
105 <option value="PepsinA + P">PepsinA + P</option> 104 <option value="PepsinA + P">PepsinA + P</option>
106 <option value="cyanogen-bromide">cyanogen-bromide</option> 105 <option value="cyanogen-bromide">cyanogen-bromide</option>
107 <option value="Clostripain/P">Clostripain/P</option> 106 <option value="Clostripain/P">Clostripain/P</option>
108 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> 107 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
109 <option value="no cleavage">no cleavage</option> 108 <option value="no cleavage">no cleavage</option>
110 <option value="unspecific cleavage">unspecific cleavage</option> 109 <option value="unspecific cleavage">unspecific cleavage</option>
111 <option value="Formic_acid">Formic_acid</option>
112 <option value="Lys-C">Lys-C</option>
113 <option value="Lys-N">Lys-N</option>
114 <option value="Lys-C/P">Lys-C/P</option> 110 <option value="Lys-C/P">Lys-C/P</option>
111 <option value="PepsinA">PepsinA</option>
112 <option value="TrypChymo">TrypChymo</option>
115 <option value="Trypsin">Trypsin</option> 113 <option value="Trypsin">Trypsin</option>
116 <expand macro="list_string_san"/> 114 <expand macro="list_string_san" name="name"/>
117 </param> 115 </param>
118 <param name="specificity" argument="-enzyme:specificity" display="radio" type="select" optional="false" label="Specificity of the enzyme" help="Default: deduce from input.. 'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context (enzyme is irrelevant)"> 116 <param name="specificity" argument="-enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input.. 'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
119 <option value="auto" selected="true">auto</option> 117 <option value="auto" selected="true">auto</option>
120 <option value="full">full</option> 118 <option value="full">full</option>
121 <option value="semi">semi</option> 119 <option value="semi">semi</option>
122 <option value="none">none</option> 120 <option value="none">none</option>
123 <expand macro="list_string_san"/> 121 <expand macro="list_string_san" name="specificity"/>
124 </param> 122 </param>
125 </section> 123 </section>
126 <expand macro="adv_opts_macro"> 124 <expand macro="adv_opts_macro">
127 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 125 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
128 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 126 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
129 <expand macro="list_string_san"/> 127 <expand macro="list_string_san" name="test"/>
130 </param> 128 </param>
131 </expand> 129 </expand>
132 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 130 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
133 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 131 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
134 </param> 132 </param>
137 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 135 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
138 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 136 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
139 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 137 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
140 </data> 138 </data>
141 </outputs> 139 </outputs>
142 <tests> 140 <tests><!-- TOPP_PeptideIndexer_1 -->
143 <expand macro="autotest_PeptideIndexer"/> 141 <test expect_num_outputs="2">
144 <expand macro="manutest_PeptideIndexer"/> 142 <section name="adv_opts">
143 <param name="force" value="false"/>
144 <param name="test" value="true"/>
145 </section>
146 <param name="in" value="PeptideIndexer_1.idXML"/>
147 <param name="fasta" value="PeptideIndexer_1.fasta"/>
148 <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
149 <param name="decoy_string" value=""/>
150 <param name="decoy_string_position" value="prefix"/>
151 <param name="missing_decoy_action" value="error"/>
152 <param name="write_protein_sequence" value="false"/>
153 <param name="write_protein_description" value="false"/>
154 <param name="keep_unreferenced_proteins" value="false"/>
155 <param name="unmatched_action" value="warn"/>
156 <param name="aaa_max" value="4"/>
157 <param name="mismatches_max" value="0"/>
158 <param name="IL_equivalent" value="false"/>
159 <section name="enzyme">
160 <param name="name" value="auto"/>
161 <param name="specificity" value="none"/>
162 </section>
163 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
164 <output name="ctd_out" ftype="xml">
165 <assert_contents>
166 <is_valid_xml/>
167 </assert_contents>
168 </output>
169 </test>
170 <!-- TOPP_PeptideIndexer_2 -->
171 <test expect_num_outputs="2">
172 <section name="adv_opts">
173 <param name="force" value="false"/>
174 <param name="test" value="true"/>
175 </section>
176 <param name="in" value="PeptideIndexer_1.idXML"/>
177 <param name="fasta" value="PeptideIndexer_1.fasta"/>
178 <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
179 <param name="decoy_string" value=""/>
180 <param name="decoy_string_position" value="prefix"/>
181 <param name="missing_decoy_action" value="error"/>
182 <param name="write_protein_sequence" value="true"/>
183 <param name="write_protein_description" value="false"/>
184 <param name="keep_unreferenced_proteins" value="false"/>
185 <param name="unmatched_action" value="warn"/>
186 <param name="aaa_max" value="4"/>
187 <param name="mismatches_max" value="0"/>
188 <param name="IL_equivalent" value="false"/>
189 <section name="enzyme">
190 <param name="name" value="auto"/>
191 <param name="specificity" value="none"/>
192 </section>
193 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
194 <output name="ctd_out" ftype="xml">
195 <assert_contents>
196 <is_valid_xml/>
197 </assert_contents>
198 </output>
199 </test>
200 <!-- TOPP_PeptideIndexer_3 -->
201 <test expect_num_outputs="2">
202 <section name="adv_opts">
203 <param name="force" value="false"/>
204 <param name="test" value="true"/>
205 </section>
206 <param name="in" value="PeptideIndexer_1.idXML"/>
207 <param name="fasta" value="PeptideIndexer_1.fasta"/>
208 <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
209 <param name="decoy_string" value=""/>
210 <param name="decoy_string_position" value="prefix"/>
211 <param name="missing_decoy_action" value="error"/>
212 <param name="write_protein_sequence" value="false"/>
213 <param name="write_protein_description" value="false"/>
214 <param name="keep_unreferenced_proteins" value="true"/>
215 <param name="unmatched_action" value="warn"/>
216 <param name="aaa_max" value="4"/>
217 <param name="mismatches_max" value="0"/>
218 <param name="IL_equivalent" value="false"/>
219 <section name="enzyme">
220 <param name="name" value="auto"/>
221 <param name="specificity" value="none"/>
222 </section>
223 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
224 <output name="ctd_out" ftype="xml">
225 <assert_contents>
226 <is_valid_xml/>
227 </assert_contents>
228 </output>
229 </test>
230 <!-- TOPP_PeptideIndexer_4 -->
231 <test expect_num_outputs="2">
232 <section name="adv_opts">
233 <param name="force" value="false"/>
234 <param name="test" value="true"/>
235 </section>
236 <param name="in" value="PeptideIndexer_1.idXML"/>
237 <param name="fasta" value="PeptideIndexer_1.fasta"/>
238 <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
239 <param name="decoy_string" value=""/>
240 <param name="decoy_string_position" value="prefix"/>
241 <param name="missing_decoy_action" value="error"/>
242 <param name="write_protein_sequence" value="true"/>
243 <param name="write_protein_description" value="false"/>
244 <param name="keep_unreferenced_proteins" value="false"/>
245 <param name="unmatched_action" value="warn"/>
246 <param name="aaa_max" value="0"/>
247 <param name="mismatches_max" value="0"/>
248 <param name="IL_equivalent" value="false"/>
249 <section name="enzyme">
250 <param name="name" value="auto"/>
251 <param name="specificity" value="none"/>
252 </section>
253 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
254 <output name="ctd_out" ftype="xml">
255 <assert_contents>
256 <is_valid_xml/>
257 </assert_contents>
258 </output>
259 </test>
260 <!-- TOPP_PeptideIndexer_5 -->
261 <test expect_num_outputs="2">
262 <section name="adv_opts">
263 <param name="force" value="false"/>
264 <param name="test" value="true"/>
265 </section>
266 <param name="in" value="PeptideIndexer_1.idXML"/>
267 <param name="fasta" value="PeptideIndexer_1.fasta"/>
268 <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
269 <param name="decoy_string" value=""/>
270 <param name="decoy_string_position" value="prefix"/>
271 <param name="missing_decoy_action" value="error"/>
272 <param name="write_protein_sequence" value="false"/>
273 <param name="write_protein_description" value="false"/>
274 <param name="keep_unreferenced_proteins" value="false"/>
275 <param name="unmatched_action" value="warn"/>
276 <param name="aaa_max" value="4"/>
277 <param name="mismatches_max" value="0"/>
278 <param name="IL_equivalent" value="false"/>
279 <section name="enzyme">
280 <param name="name" value="auto"/>
281 <param name="specificity" value="none"/>
282 </section>
283 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
284 <output name="ctd_out" ftype="xml">
285 <assert_contents>
286 <is_valid_xml/>
287 </assert_contents>
288 </output>
289 </test>
290 <!-- TOPP_PeptideIndexer_6 -->
291 <test expect_num_outputs="2">
292 <section name="adv_opts">
293 <param name="force" value="false"/>
294 <param name="test" value="true"/>
295 </section>
296 <param name="in" value="PeptideIndexer_2.idXML"/>
297 <param name="fasta" value="PeptideIndexer_1.fasta"/>
298 <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
299 <param name="decoy_string" value=""/>
300 <param name="decoy_string_position" value="prefix"/>
301 <param name="missing_decoy_action" value="error"/>
302 <param name="write_protein_sequence" value="false"/>
303 <param name="write_protein_description" value="false"/>
304 <param name="keep_unreferenced_proteins" value="false"/>
305 <param name="unmatched_action" value="warn"/>
306 <param name="aaa_max" value="3"/>
307 <param name="mismatches_max" value="0"/>
308 <param name="IL_equivalent" value="false"/>
309 <section name="enzyme">
310 <param name="name" value="auto"/>
311 <param name="specificity" value="none"/>
312 </section>
313 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
314 <output name="ctd_out" ftype="xml">
315 <assert_contents>
316 <is_valid_xml/>
317 </assert_contents>
318 </output>
319 </test>
320 <!-- TOPP_PeptideIndexer_7 -->
321 <test expect_num_outputs="2">
322 <section name="adv_opts">
323 <param name="force" value="false"/>
324 <param name="test" value="true"/>
325 </section>
326 <param name="in" value="PeptideIndexer_3.idXML"/>
327 <param name="fasta" value="PeptideIndexer_1.fasta"/>
328 <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
329 <param name="decoy_string" value="DECOY_"/>
330 <param name="decoy_string_position" value="prefix"/>
331 <param name="missing_decoy_action" value="error"/>
332 <param name="write_protein_sequence" value="false"/>
333 <param name="write_protein_description" value="false"/>
334 <param name="keep_unreferenced_proteins" value="false"/>
335 <param name="unmatched_action" value="warn"/>
336 <param name="aaa_max" value="4"/>
337 <param name="mismatches_max" value="0"/>
338 <param name="IL_equivalent" value="false"/>
339 <section name="enzyme">
340 <param name="name" value="auto"/>
341 <param name="specificity" value="full"/>
342 </section>
343 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
344 <output name="ctd_out" ftype="xml">
345 <assert_contents>
346 <is_valid_xml/>
347 </assert_contents>
348 </output>
349 </test>
350 <!-- TOPP_PeptideIndexer_8 -->
351 <test expect_num_outputs="2">
352 <section name="adv_opts">
353 <param name="force" value="false"/>
354 <param name="test" value="true"/>
355 </section>
356 <param name="in" value="PeptideIndexer_3.idXML"/>
357 <param name="fasta" value="PeptideIndexer_1.fasta"/>
358 <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
359 <param name="decoy_string" value=""/>
360 <param name="decoy_string_position" value="prefix"/>
361 <param name="missing_decoy_action" value="error"/>
362 <param name="write_protein_sequence" value="false"/>
363 <param name="write_protein_description" value="false"/>
364 <param name="keep_unreferenced_proteins" value="false"/>
365 <param name="unmatched_action" value="warn"/>
366 <param name="aaa_max" value="4"/>
367 <param name="mismatches_max" value="0"/>
368 <param name="IL_equivalent" value="false"/>
369 <section name="enzyme">
370 <param name="name" value="auto"/>
371 <param name="specificity" value="semi"/>
372 </section>
373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
374 <output name="ctd_out" ftype="xml">
375 <assert_contents>
376 <is_valid_xml/>
377 </assert_contents>
378 </output>
379 </test>
380 <!-- TOPP_PeptideIndexer_9 -->
381 <test expect_num_outputs="2">
382 <section name="adv_opts">
383 <param name="force" value="false"/>
384 <param name="test" value="true"/>
385 </section>
386 <param name="in" value="PeptideIndexer_3.idXML"/>
387 <param name="fasta" value="PeptideIndexer_1.fasta"/>
388 <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
389 <param name="decoy_string" value=""/>
390 <param name="decoy_string_position" value="prefix"/>
391 <param name="missing_decoy_action" value="error"/>
392 <param name="write_protein_sequence" value="false"/>
393 <param name="write_protein_description" value="false"/>
394 <param name="keep_unreferenced_proteins" value="false"/>
395 <param name="unmatched_action" value="remove"/>
396 <param name="aaa_max" value="4"/>
397 <param name="mismatches_max" value="0"/>
398 <param name="IL_equivalent" value="false"/>
399 <section name="enzyme">
400 <param name="name" value="auto"/>
401 <param name="specificity" value="none"/>
402 </section>
403 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
404 <output name="ctd_out" ftype="xml">
405 <assert_contents>
406 <is_valid_xml/>
407 </assert_contents>
408 </output>
409 </test>
410 <!-- TOPP_PeptideIndexer_10 -->
411 <test expect_num_outputs="2">
412 <section name="adv_opts">
413 <param name="force" value="false"/>
414 <param name="test" value="true"/>
415 </section>
416 <param name="in" value="PeptideIndexer_10_input.idXML"/>
417 <param name="fasta" value="PeptideIndexer_10_input.fasta"/>
418 <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
419 <param name="decoy_string" value=""/>
420 <param name="decoy_string_position" value="prefix"/>
421 <param name="missing_decoy_action" value="error"/>
422 <param name="write_protein_sequence" value="true"/>
423 <param name="write_protein_description" value="false"/>
424 <param name="keep_unreferenced_proteins" value="false"/>
425 <param name="unmatched_action" value="error"/>
426 <param name="aaa_max" value="3"/>
427 <param name="mismatches_max" value="0"/>
428 <param name="IL_equivalent" value="true"/>
429 <section name="enzyme">
430 <param name="name" value="auto"/>
431 <param name="specificity" value="auto"/>
432 </section>
433 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
434 <output name="ctd_out" ftype="xml">
435 <assert_contents>
436 <is_valid_xml/>
437 </assert_contents>
438 </output>
439 </test>
440 <!-- TOPP_PeptideIndexer_12 -->
441 <test expect_num_outputs="2">
442 <section name="adv_opts">
443 <param name="force" value="false"/>
444 <param name="test" value="true"/>
445 </section>
446 <param name="in" value="PeptideIndexer_1.idXML"/>
447 <param name="fasta" value="PeptideIndexer_1.fasta"/>
448 <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
449 <param name="decoy_string" value=""/>
450 <param name="decoy_string_position" value="prefix"/>
451 <param name="missing_decoy_action" value="error"/>
452 <param name="write_protein_sequence" value="false"/>
453 <param name="write_protein_description" value="false"/>
454 <param name="keep_unreferenced_proteins" value="false"/>
455 <param name="unmatched_action" value="warn"/>
456 <param name="aaa_max" value="4"/>
457 <param name="mismatches_max" value="0"/>
458 <param name="IL_equivalent" value="false"/>
459 <section name="enzyme">
460 <param name="name" value="auto"/>
461 <param name="specificity" value="none"/>
462 </section>
463 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
464 <output name="ctd_out" ftype="xml">
465 <assert_contents>
466 <is_valid_xml/>
467 </assert_contents>
468 </output>
469 </test>
470 <!-- TOPP_PeptideIndexer_13 -->
471 <test expect_num_outputs="2">
472 <section name="adv_opts">
473 <param name="force" value="false"/>
474 <param name="test" value="true"/>
475 </section>
476 <param name="in" value="empty.idXML"/>
477 <param name="fasta" value="PeptideIndexer_1.fasta"/>
478 <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
479 <param name="decoy_string" value=""/>
480 <param name="decoy_string_position" value="prefix"/>
481 <param name="missing_decoy_action" value="error"/>
482 <param name="write_protein_sequence" value="false"/>
483 <param name="write_protein_description" value="false"/>
484 <param name="keep_unreferenced_proteins" value="false"/>
485 <param name="unmatched_action" value="error"/>
486 <param name="aaa_max" value="4"/>
487 <param name="mismatches_max" value="0"/>
488 <param name="IL_equivalent" value="false"/>
489 <section name="enzyme">
490 <param name="name" value="auto"/>
491 <param name="specificity" value="auto"/>
492 </section>
493 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
494 <output name="ctd_out" ftype="xml">
495 <assert_contents>
496 <is_valid_xml/>
497 </assert_contents>
498 </output>
499 </test>
500 <!-- TOPP_PeptideIndexer_14 -->
501 <test expect_num_outputs="2">
502 <section name="adv_opts">
503 <param name="force" value="false"/>
504 <param name="test" value="true"/>
505 </section>
506 <param name="in" value="PeptideIndexer_14.idXML"/>
507 <param name="fasta" value="PeptideIndexer_2.fasta"/>
508 <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
509 <param name="decoy_string" value=""/>
510 <param name="decoy_string_position" value="prefix"/>
511 <param name="missing_decoy_action" value="error"/>
512 <param name="write_protein_sequence" value="true"/>
513 <param name="write_protein_description" value="false"/>
514 <param name="keep_unreferenced_proteins" value="false"/>
515 <param name="unmatched_action" value="error"/>
516 <param name="aaa_max" value="4"/>
517 <param name="mismatches_max" value="0"/>
518 <param name="IL_equivalent" value="false"/>
519 <section name="enzyme">
520 <param name="name" value="auto"/>
521 <param name="specificity" value="none"/>
522 </section>
523 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
524 <output name="ctd_out" ftype="xml">
525 <assert_contents>
526 <is_valid_xml/>
527 </assert_contents>
528 </output>
529 </test>
145 </tests> 530 </tests>
146 <help><![CDATA[Refreshes the protein references for all peptide hits. 531 <help><![CDATA[Refreshes the protein references for all peptide hits.
147 532
148 533
149 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PeptideIndexer.html]]></help> 534 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PeptideIndexer.html]]></help>
150 <expand macro="references"/> 535 <expand macro="references"/>
151 </tool> 536 </tool>