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comparison PeptideIndexer.xml @ 14:0693b186f39e 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 21:45:45 +0000
parents d6aca689dd48
children
comparison
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13:d6aca689dd48 14:0693b186f39e
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: [ID Processing]--> 2 <!--Proposed Tool Section: [Identification Processing]-->
4 <tool id="PeptideIndexer" name="PeptideIndexer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Refreshes the protein references for all peptide hits</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">PeptideIndexer</token> 6 <token name="@EXECUTABLE@">PeptideIndexer</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 #if $fasta: 18 #if $fasta:
20 mkdir fasta && 19 mkdir fasta &&
21 ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && 20 cp '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
22 #end if 21 #end if
23 mkdir out && 22 mkdir out &&
24 23
25 ## Main program call 24 ## Main program call
26 25
45 <configfiles> 44 <configfiles>
46 <inputs name="args_json" data_style="paths"/> 45 <inputs name="args_json" data_style="paths"/>
47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 46 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
48 </configfiles> 47 </configfiles>
49 <inputs> 48 <inputs>
50 <param argument="-in" type="data" format="idxml" optional="false" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/> 49 <param argument="-in" type="data" format="idxml" label="Input idXML file containing the identifications" help=" select idxml 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)"/> 50 <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)"/>
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)"> 51 <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)">
53 <expand macro="list_string_san" name="decoy_string"/> 52 <expand macro="list_string_san" name="decoy_string"/>
54 </param> 53 </param>
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)"> 54 <param argument="-decoy_string_position" type="select" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
56 <option value="prefix" selected="true">prefix</option> 55 <option value="prefix" selected="true">prefix</option>
57 <option value="suffix">suffix</option> 56 <option value="suffix">suffix</option>
58 <expand macro="list_string_san" name="decoy_string_position"/> 57 <expand macro="list_string_san" name="decoy_string_position"/>
59 </param> 58 </param>
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=""> 59 <param argument="-missing_decoy_action" type="select" 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="">
61 <option value="error" selected="true">error</option> 60 <option value="error" selected="true">error</option>
62 <option value="warn">warn</option> 61 <option value="warn">warn</option>
63 <option value="silent">silent</option> 62 <option value="silent">silent</option>
64 <expand macro="list_string_san" name="missing_decoy_action"/> 63 <expand macro="list_string_san" name="missing_decoy_action"/>
65 </param> 64 </param>
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=""/> 65 <param argument="-write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are 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=""/> 66 <param argument="-write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" 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=""/> 67 <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=""/>
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=""> 68 <param argument="-unmatched_action" type="select" 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="">
70 <option value="error" selected="true">error</option> 69 <option value="error" selected="true">error</option>
71 <option value="warn">warn</option> 70 <option value="warn">warn</option>
72 <option value="remove">remove</option> 71 <option value="remove">remove</option>
73 <expand macro="list_string_san" name="unmatched_action"/> 72 <expand macro="list_string_san" name="unmatched_action"/>
74 </param> 73 </param>
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'"/> 74 <param argument="-aaa_max" type="integer" 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'"/>
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"/> 75 <param argument="-mismatches_max" type="integer" 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"/>
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"/> 76 <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"/>
77 <param argument="-allow_nterm_protein_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Allow the protein N-terminus amino acid to clip" help=""/>
78 <section name="enzyme" title="" help="" expanded="false"> 78 <section name="enzyme" title="" help="" expanded="false">
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"> 79 <param name="name" argument="-enzyme:name" type="select" 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">
80 <option value="auto" selected="true">auto</option> 80 <option value="auto" selected="true">auto</option>
81 <option value="Trypsin">Trypsin</option>
81 <option value="Arg-C">Arg-C</option> 82 <option value="Arg-C">Arg-C</option>
83 <option value="cyanogen-bromide">cyanogen-bromide</option>
84 <option value="Clostripain/P">Clostripain/P</option>
85 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
86 <option value="no cleavage">no cleavage</option>
87 <option value="unspecific cleavage">unspecific cleavage</option>
88 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
89 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
90 <option value="2-iodobenzoate">2-iodobenzoate</option>
91 <option value="iodosobenzoate">iodosobenzoate</option>
92 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
93 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
94 <option value="Glu-C+P">Glu-C+P</option>
95 <option value="PepsinA + P">PepsinA + P</option>
96 <option value="Trypsin/P">Trypsin/P</option>
97 <option value="V8-DE">V8-DE</option>
82 <option value="Arg-C/P">Arg-C/P</option> 98 <option value="Arg-C/P">Arg-C/P</option>
83 <option value="Asp-N">Asp-N</option> 99 <option value="Asp-N">Asp-N</option>
84 <option value="Asp-N/B">Asp-N/B</option> 100 <option value="Asp-N/B">Asp-N/B</option>
85 <option value="Asp-N_ambic">Asp-N_ambic</option> 101 <option value="Asp-N_ambic">Asp-N_ambic</option>
86 <option value="Chymotrypsin">Chymotrypsin</option> 102 <option value="Chymotrypsin">Chymotrypsin</option>
87 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 103 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
88 <option value="CNBr">CNBr</option> 104 <option value="CNBr">CNBr</option>
89 <option value="Formic_acid">Formic_acid</option> 105 <option value="Formic_acid">Formic_acid</option>
90 <option value="Lys-C">Lys-C</option> 106 <option value="Lys-C">Lys-C</option>
91 <option value="Lys-N">Lys-N</option> 107 <option value="Lys-N">Lys-N</option>
92 <option value="Trypsin/P">Trypsin/P</option> 108 <option value="Lys-C/P">Lys-C/P</option>
93 <option value="V8-DE">V8-DE</option> 109 <option value="PepsinA">PepsinA</option>
110 <option value="TrypChymo">TrypChymo</option>
94 <option value="V8-E">V8-E</option> 111 <option value="V8-E">V8-E</option>
95 <option value="leukocyte elastase">leukocyte elastase</option> 112 <option value="leukocyte elastase">leukocyte elastase</option>
96 <option value="proline endopeptidase">proline endopeptidase</option> 113 <option value="proline endopeptidase">proline endopeptidase</option>
97 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
98 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
99 <option value="2-iodobenzoate">2-iodobenzoate</option>
100 <option value="iodosobenzoate">iodosobenzoate</option>
101 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
102 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
103 <option value="Glu-C+P">Glu-C+P</option>
104 <option value="PepsinA + P">PepsinA + P</option>
105 <option value="cyanogen-bromide">cyanogen-bromide</option>
106 <option value="Clostripain/P">Clostripain/P</option>
107 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
108 <option value="no cleavage">no cleavage</option>
109 <option value="unspecific cleavage">unspecific cleavage</option>
110 <option value="Lys-C/P">Lys-C/P</option>
111 <option value="PepsinA">PepsinA</option>
112 <option value="TrypChymo">TrypChymo</option>
113 <option value="Trypsin">Trypsin</option>
114 <expand macro="list_string_san" name="name"/> 114 <expand macro="list_string_san" name="name"/>
115 </param> 115 </param>
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)"> 116 <param name="specificity" argument="-enzyme:specificity" type="select" 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)">
117 <option value="auto" selected="true">auto</option> 117 <option value="auto" selected="true">auto</option>
118 <option value="full">full</option> 118 <option value="full">full</option>
119 <option value="semi">semi</option> 119 <option value="semi">semi</option>
120 <option value="none">none</option> 120 <option value="none">none</option>
121 <expand macro="list_string_san" name="specificity"/> 121 <expand macro="list_string_san" name="specificity"/>
122 </param> 122 </param>
123 </section> 123 </section>
124 <expand macro="adv_opts_macro"> 124 <expand macro="adv_opts_macro">
125 <param 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=""/>
126 <param 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" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
127 <expand macro="list_string_san" name="test"/> 127 <expand macro="list_string_san" name="test"/>
128 </param> 128 </param>
129 </expand> 129 </expand>
130 <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">
131 <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>
135 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 135 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
136 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 136 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
137 <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>
138 </data> 138 </data>
139 </outputs> 139 </outputs>
140 <tests><!-- TOPP_PeptideIndexer_1 --> 140 <tests>
141 <!-- TOPP_PeptideIndexer_1 -->
141 <test expect_num_outputs="2"> 142 <test expect_num_outputs="2">
142 <section name="adv_opts"> 143 <section name="adv_opts">
143 <param name="force" value="false"/> 144 <param name="force" value="false"/>
144 <param name="test" value="true"/> 145 <param name="test" value="true"/>
145 </section> 146 </section>
146 <param name="in" value="PeptideIndexer_1.idXML"/> 147 <param name="in" value="PeptideIndexer_1.idXML"/>
147 <param name="fasta" value="PeptideIndexer_1.fasta"/> 148 <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 <output name="out" value="PeptideIndexer_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
149 <param name="decoy_string" value=""/> 150 <param name="decoy_string" value=""/>
150 <param name="decoy_string_position" value="prefix"/> 151 <param name="decoy_string_position" value="prefix"/>
151 <param name="missing_decoy_action" value="error"/> 152 <param name="missing_decoy_action" value="error"/>
152 <param name="write_protein_sequence" value="false"/> 153 <param name="write_protein_sequence" value="false"/>
153 <param name="write_protein_description" value="false"/> 154 <param name="write_protein_description" value="false"/>
154 <param name="keep_unreferenced_proteins" value="false"/> 155 <param name="keep_unreferenced_proteins" value="false"/>
155 <param name="unmatched_action" value="warn"/> 156 <param name="unmatched_action" value="warn"/>
156 <param name="aaa_max" value="4"/> 157 <param name="aaa_max" value="4"/>
157 <param name="mismatches_max" value="0"/> 158 <param name="mismatches_max" value="0"/>
158 <param name="IL_equivalent" value="false"/> 159 <param name="IL_equivalent" value="false"/>
159 <section name="enzyme"> 160 <param name="allow_nterm_protein_cleavage" value="true"/>
160 <param name="name" value="auto"/> 161 <section name="enzyme">
161 <param name="specificity" value="none"/> 162 <param name="name" value="auto"/>
162 </section> 163 <param name="specificity" value="none"/>
163 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 164 </section>
164 <output name="ctd_out" ftype="xml"> 165 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
165 <assert_contents> 166 <output name="ctd_out" ftype="xml">
166 <is_valid_xml/> 167 <assert_contents>
167 </assert_contents> 168 <is_valid_xml/>
168 </output> 169 </assert_contents>
170 </output>
171 <assert_stdout>
172 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
173 </assert_stdout>
169 </test> 174 </test>
170 <!-- TOPP_PeptideIndexer_2 --> 175 <!-- TOPP_PeptideIndexer_2 -->
171 <test expect_num_outputs="2"> 176 <test expect_num_outputs="2">
172 <section name="adv_opts"> 177 <section name="adv_opts">
173 <param name="force" value="false"/> 178 <param name="force" value="false"/>
174 <param name="test" value="true"/> 179 <param name="test" value="true"/>
175 </section> 180 </section>
176 <param name="in" value="PeptideIndexer_1.idXML"/> 181 <param name="in" value="PeptideIndexer_1.idXML"/>
177 <param name="fasta" value="PeptideIndexer_1.fasta"/> 182 <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"/> 183 <output name="out" value="PeptideIndexer_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
179 <param name="decoy_string" value=""/> 184 <param name="decoy_string" value=""/>
180 <param name="decoy_string_position" value="prefix"/> 185 <param name="decoy_string_position" value="prefix"/>
181 <param name="missing_decoy_action" value="error"/> 186 <param name="missing_decoy_action" value="error"/>
182 <param name="write_protein_sequence" value="true"/> 187 <param name="write_protein_sequence" value="true"/>
183 <param name="write_protein_description" value="false"/> 188 <param name="write_protein_description" value="false"/>
184 <param name="keep_unreferenced_proteins" value="false"/> 189 <param name="keep_unreferenced_proteins" value="false"/>
185 <param name="unmatched_action" value="warn"/> 190 <param name="unmatched_action" value="warn"/>
186 <param name="aaa_max" value="4"/> 191 <param name="aaa_max" value="4"/>
187 <param name="mismatches_max" value="0"/> 192 <param name="mismatches_max" value="0"/>
188 <param name="IL_equivalent" value="false"/> 193 <param name="IL_equivalent" value="false"/>
189 <section name="enzyme"> 194 <param name="allow_nterm_protein_cleavage" value="true"/>
190 <param name="name" value="auto"/> 195 <section name="enzyme">
191 <param name="specificity" value="none"/> 196 <param name="name" value="auto"/>
192 </section> 197 <param name="specificity" value="none"/>
193 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 198 </section>
194 <output name="ctd_out" ftype="xml"> 199 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
195 <assert_contents> 200 <output name="ctd_out" ftype="xml">
196 <is_valid_xml/> 201 <assert_contents>
197 </assert_contents> 202 <is_valid_xml/>
198 </output> 203 </assert_contents>
204 </output>
205 <assert_stdout>
206 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
207 </assert_stdout>
199 </test> 208 </test>
200 <!-- TOPP_PeptideIndexer_3 --> 209 <!-- TOPP_PeptideIndexer_3 -->
201 <test expect_num_outputs="2"> 210 <test expect_num_outputs="2">
202 <section name="adv_opts"> 211 <section name="adv_opts">
203 <param name="force" value="false"/> 212 <param name="force" value="false"/>
204 <param name="test" value="true"/> 213 <param name="test" value="true"/>
205 </section> 214 </section>
206 <param name="in" value="PeptideIndexer_1.idXML"/> 215 <param name="in" value="PeptideIndexer_1.idXML"/>
207 <param name="fasta" value="PeptideIndexer_1.fasta"/> 216 <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"/> 217 <output name="out" value="PeptideIndexer_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
209 <param name="decoy_string" value=""/> 218 <param name="decoy_string" value=""/>
210 <param name="decoy_string_position" value="prefix"/> 219 <param name="decoy_string_position" value="prefix"/>
211 <param name="missing_decoy_action" value="error"/> 220 <param name="missing_decoy_action" value="error"/>
212 <param name="write_protein_sequence" value="false"/> 221 <param name="write_protein_sequence" value="false"/>
213 <param name="write_protein_description" value="false"/> 222 <param name="write_protein_description" value="false"/>
214 <param name="keep_unreferenced_proteins" value="true"/> 223 <param name="keep_unreferenced_proteins" value="true"/>
215 <param name="unmatched_action" value="warn"/> 224 <param name="unmatched_action" value="warn"/>
216 <param name="aaa_max" value="4"/> 225 <param name="aaa_max" value="4"/>
217 <param name="mismatches_max" value="0"/> 226 <param name="mismatches_max" value="0"/>
218 <param name="IL_equivalent" value="false"/> 227 <param name="IL_equivalent" value="false"/>
219 <section name="enzyme"> 228 <param name="allow_nterm_protein_cleavage" value="true"/>
220 <param name="name" value="auto"/> 229 <section name="enzyme">
221 <param name="specificity" value="none"/> 230 <param name="name" value="auto"/>
222 </section> 231 <param name="specificity" value="none"/>
223 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 232 </section>
224 <output name="ctd_out" ftype="xml"> 233 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
225 <assert_contents> 234 <output name="ctd_out" ftype="xml">
226 <is_valid_xml/> 235 <assert_contents>
227 </assert_contents> 236 <is_valid_xml/>
228 </output> 237 </assert_contents>
238 </output>
239 <assert_stdout>
240 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
241 </assert_stdout>
229 </test> 242 </test>
230 <!-- TOPP_PeptideIndexer_4 --> 243 <!-- TOPP_PeptideIndexer_4 -->
231 <test expect_num_outputs="2"> 244 <test expect_num_outputs="2">
232 <section name="adv_opts"> 245 <section name="adv_opts">
233 <param name="force" value="false"/> 246 <param name="force" value="false"/>
234 <param name="test" value="true"/> 247 <param name="test" value="true"/>
235 </section> 248 </section>
236 <param name="in" value="PeptideIndexer_1.idXML"/> 249 <param name="in" value="PeptideIndexer_1.idXML"/>
237 <param name="fasta" value="PeptideIndexer_1.fasta"/> 250 <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"/> 251 <output name="out" value="PeptideIndexer_4_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
239 <param name="decoy_string" value=""/> 252 <param name="decoy_string" value=""/>
240 <param name="decoy_string_position" value="prefix"/> 253 <param name="decoy_string_position" value="prefix"/>
241 <param name="missing_decoy_action" value="error"/> 254 <param name="missing_decoy_action" value="error"/>
242 <param name="write_protein_sequence" value="true"/> 255 <param name="write_protein_sequence" value="true"/>
243 <param name="write_protein_description" value="false"/> 256 <param name="write_protein_description" value="false"/>
244 <param name="keep_unreferenced_proteins" value="false"/> 257 <param name="keep_unreferenced_proteins" value="false"/>
245 <param name="unmatched_action" value="warn"/> 258 <param name="unmatched_action" value="warn"/>
246 <param name="aaa_max" value="0"/> 259 <param name="aaa_max" value="0"/>
247 <param name="mismatches_max" value="0"/> 260 <param name="mismatches_max" value="0"/>
248 <param name="IL_equivalent" value="false"/> 261 <param name="IL_equivalent" value="false"/>
249 <section name="enzyme"> 262 <param name="allow_nterm_protein_cleavage" value="true"/>
250 <param name="name" value="auto"/> 263 <section name="enzyme">
251 <param name="specificity" value="none"/> 264 <param name="name" value="auto"/>
252 </section> 265 <param name="specificity" value="none"/>
253 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 266 </section>
254 <output name="ctd_out" ftype="xml"> 267 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
255 <assert_contents> 268 <output name="ctd_out" ftype="xml">
256 <is_valid_xml/> 269 <assert_contents>
257 </assert_contents> 270 <is_valid_xml/>
258 </output> 271 </assert_contents>
272 </output>
273 <assert_stdout>
274 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
275 </assert_stdout>
259 </test> 276 </test>
260 <!-- TOPP_PeptideIndexer_5 --> 277 <!-- TOPP_PeptideIndexer_5 -->
261 <test expect_num_outputs="2"> 278 <test expect_num_outputs="2">
262 <section name="adv_opts"> 279 <section name="adv_opts">
263 <param name="force" value="false"/> 280 <param name="force" value="false"/>
264 <param name="test" value="true"/> 281 <param name="test" value="true"/>
265 </section> 282 </section>
266 <param name="in" value="PeptideIndexer_1.idXML"/> 283 <param name="in" value="PeptideIndexer_1.idXML"/>
267 <param name="fasta" value="PeptideIndexer_1.fasta"/> 284 <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"/> 285 <output name="out" value="PeptideIndexer_5_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
269 <param name="decoy_string" value=""/> 286 <param name="decoy_string" value=""/>
270 <param name="decoy_string_position" value="prefix"/> 287 <param name="decoy_string_position" value="prefix"/>
271 <param name="missing_decoy_action" value="error"/> 288 <param name="missing_decoy_action" value="error"/>
272 <param name="write_protein_sequence" value="false"/> 289 <param name="write_protein_sequence" value="false"/>
273 <param name="write_protein_description" value="false"/> 290 <param name="write_protein_description" value="false"/>
274 <param name="keep_unreferenced_proteins" value="false"/> 291 <param name="keep_unreferenced_proteins" value="false"/>
275 <param name="unmatched_action" value="warn"/> 292 <param name="unmatched_action" value="warn"/>
276 <param name="aaa_max" value="4"/> 293 <param name="aaa_max" value="4"/>
277 <param name="mismatches_max" value="0"/> 294 <param name="mismatches_max" value="0"/>
278 <param name="IL_equivalent" value="false"/> 295 <param name="IL_equivalent" value="false"/>
279 <section name="enzyme"> 296 <param name="allow_nterm_protein_cleavage" value="true"/>
280 <param name="name" value="auto"/> 297 <section name="enzyme">
281 <param name="specificity" value="none"/> 298 <param name="name" value="auto"/>
282 </section> 299 <param name="specificity" value="none"/>
283 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 300 </section>
284 <output name="ctd_out" ftype="xml"> 301 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
285 <assert_contents> 302 <output name="ctd_out" ftype="xml">
286 <is_valid_xml/> 303 <assert_contents>
287 </assert_contents> 304 <is_valid_xml/>
288 </output> 305 </assert_contents>
306 </output>
307 <assert_stdout>
308 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
309 </assert_stdout>
289 </test> 310 </test>
290 <!-- TOPP_PeptideIndexer_6 --> 311 <!-- TOPP_PeptideIndexer_6 -->
291 <test expect_num_outputs="2"> 312 <test expect_num_outputs="2">
292 <section name="adv_opts"> 313 <section name="adv_opts">
293 <param name="force" value="false"/> 314 <param name="force" value="false"/>
294 <param name="test" value="true"/> 315 <param name="test" value="true"/>
295 </section> 316 </section>
296 <param name="in" value="PeptideIndexer_2.idXML"/> 317 <param name="in" value="PeptideIndexer_2.idXML"/>
297 <param name="fasta" value="PeptideIndexer_1.fasta"/> 318 <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"/> 319 <output name="out" value="PeptideIndexer_6_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
299 <param name="decoy_string" value=""/> 320 <param name="decoy_string" value=""/>
300 <param name="decoy_string_position" value="prefix"/> 321 <param name="decoy_string_position" value="prefix"/>
301 <param name="missing_decoy_action" value="error"/> 322 <param name="missing_decoy_action" value="error"/>
302 <param name="write_protein_sequence" value="false"/> 323 <param name="write_protein_sequence" value="false"/>
303 <param name="write_protein_description" value="false"/> 324 <param name="write_protein_description" value="false"/>
304 <param name="keep_unreferenced_proteins" value="false"/> 325 <param name="keep_unreferenced_proteins" value="false"/>
305 <param name="unmatched_action" value="warn"/> 326 <param name="unmatched_action" value="warn"/>
306 <param name="aaa_max" value="3"/> 327 <param name="aaa_max" value="3"/>
307 <param name="mismatches_max" value="0"/> 328 <param name="mismatches_max" value="0"/>
308 <param name="IL_equivalent" value="false"/> 329 <param name="IL_equivalent" value="false"/>
309 <section name="enzyme"> 330 <param name="allow_nterm_protein_cleavage" value="true"/>
310 <param name="name" value="auto"/> 331 <section name="enzyme">
311 <param name="specificity" value="none"/> 332 <param name="name" value="auto"/>
312 </section> 333 <param name="specificity" value="none"/>
313 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 334 </section>
314 <output name="ctd_out" ftype="xml"> 335 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
315 <assert_contents> 336 <output name="ctd_out" ftype="xml">
316 <is_valid_xml/> 337 <assert_contents>
317 </assert_contents> 338 <is_valid_xml/>
318 </output> 339 </assert_contents>
340 </output>
341 <assert_stdout>
342 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
343 </assert_stdout>
319 </test> 344 </test>
320 <!-- TOPP_PeptideIndexer_7 --> 345 <!-- TOPP_PeptideIndexer_7 -->
321 <test expect_num_outputs="2"> 346 <test expect_num_outputs="2">
322 <section name="adv_opts"> 347 <section name="adv_opts">
323 <param name="force" value="false"/> 348 <param name="force" value="false"/>
324 <param name="test" value="true"/> 349 <param name="test" value="true"/>
325 </section> 350 </section>
326 <param name="in" value="PeptideIndexer_3.idXML"/> 351 <param name="in" value="PeptideIndexer_3.idXML"/>
327 <param name="fasta" value="PeptideIndexer_1.fasta"/> 352 <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"/> 353 <output name="out" value="PeptideIndexer_7_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
329 <param name="decoy_string" value="DECOY_"/> 354 <param name="decoy_string" value="DECOY_"/>
330 <param name="decoy_string_position" value="prefix"/> 355 <param name="decoy_string_position" value="prefix"/>
331 <param name="missing_decoy_action" value="error"/> 356 <param name="missing_decoy_action" value="error"/>
332 <param name="write_protein_sequence" value="false"/> 357 <param name="write_protein_sequence" value="false"/>
333 <param name="write_protein_description" value="false"/> 358 <param name="write_protein_description" value="false"/>
334 <param name="keep_unreferenced_proteins" value="false"/> 359 <param name="keep_unreferenced_proteins" value="false"/>
335 <param name="unmatched_action" value="warn"/> 360 <param name="unmatched_action" value="warn"/>
336 <param name="aaa_max" value="4"/> 361 <param name="aaa_max" value="4"/>
337 <param name="mismatches_max" value="0"/> 362 <param name="mismatches_max" value="0"/>
338 <param name="IL_equivalent" value="false"/> 363 <param name="IL_equivalent" value="false"/>
364 <param name="allow_nterm_protein_cleavage" value="true"/>
339 <section name="enzyme"> 365 <section name="enzyme">
340 <param name="name" value="auto"/> 366 <param name="name" value="auto"/>
341 <param name="specificity" value="full"/> 367 <param name="specificity" value="full"/>
342 </section> 368 </section>
343 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 369 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
344 <output name="ctd_out" ftype="xml"> 370 <output name="ctd_out" ftype="xml">
345 <assert_contents> 371 <assert_contents>
346 <is_valid_xml/> 372 <is_valid_xml/>
347 </assert_contents> 373 </assert_contents>
348 </output> 374 </output>
375 <assert_stdout>
376 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
377 </assert_stdout>
349 </test> 378 </test>
350 <!-- TOPP_PeptideIndexer_8 --> 379 <!-- TOPP_PeptideIndexer_8 -->
351 <test expect_num_outputs="2"> 380 <test expect_num_outputs="2">
352 <section name="adv_opts"> 381 <section name="adv_opts">
353 <param name="force" value="false"/> 382 <param name="force" value="false"/>
354 <param name="test" value="true"/> 383 <param name="test" value="true"/>
355 </section> 384 </section>
356 <param name="in" value="PeptideIndexer_3.idXML"/> 385 <param name="in" value="PeptideIndexer_3.idXML"/>
357 <param name="fasta" value="PeptideIndexer_1.fasta"/> 386 <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"/> 387 <output name="out" value="PeptideIndexer_8_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
359 <param name="decoy_string" value=""/> 388 <param name="decoy_string" value=""/>
360 <param name="decoy_string_position" value="prefix"/> 389 <param name="decoy_string_position" value="prefix"/>
361 <param name="missing_decoy_action" value="error"/> 390 <param name="missing_decoy_action" value="error"/>
362 <param name="write_protein_sequence" value="false"/> 391 <param name="write_protein_sequence" value="false"/>
363 <param name="write_protein_description" value="false"/> 392 <param name="write_protein_description" value="false"/>
364 <param name="keep_unreferenced_proteins" value="false"/> 393 <param name="keep_unreferenced_proteins" value="false"/>
365 <param name="unmatched_action" value="warn"/> 394 <param name="unmatched_action" value="warn"/>
366 <param name="aaa_max" value="4"/> 395 <param name="aaa_max" value="4"/>
367 <param name="mismatches_max" value="0"/> 396 <param name="mismatches_max" value="0"/>
368 <param name="IL_equivalent" value="false"/> 397 <param name="IL_equivalent" value="false"/>
398 <param name="allow_nterm_protein_cleavage" value="true"/>
369 <section name="enzyme"> 399 <section name="enzyme">
370 <param name="name" value="auto"/> 400 <param name="name" value="auto"/>
371 <param name="specificity" value="semi"/> 401 <param name="specificity" value="semi"/>
372 </section> 402 </section>
373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 403 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
374 <output name="ctd_out" ftype="xml"> 404 <output name="ctd_out" ftype="xml">
375 <assert_contents> 405 <assert_contents>
376 <is_valid_xml/> 406 <is_valid_xml/>
377 </assert_contents> 407 </assert_contents>
378 </output> 408 </output>
409 <assert_stdout>
410 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
411 </assert_stdout>
379 </test> 412 </test>
380 <!-- TOPP_PeptideIndexer_9 --> 413 <!-- TOPP_PeptideIndexer_9 -->
381 <test expect_num_outputs="2"> 414 <test expect_num_outputs="2">
382 <section name="adv_opts"> 415 <section name="adv_opts">
383 <param name="force" value="false"/> 416 <param name="force" value="false"/>
384 <param name="test" value="true"/> 417 <param name="test" value="true"/>
385 </section> 418 </section>
386 <param name="in" value="PeptideIndexer_3.idXML"/> 419 <param name="in" value="PeptideIndexer_3.idXML"/>
387 <param name="fasta" value="PeptideIndexer_1.fasta"/> 420 <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"/> 421 <output name="out" value="PeptideIndexer_9_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
389 <param name="decoy_string" value=""/> 422 <param name="decoy_string" value=""/>
390 <param name="decoy_string_position" value="prefix"/> 423 <param name="decoy_string_position" value="prefix"/>
391 <param name="missing_decoy_action" value="error"/> 424 <param name="missing_decoy_action" value="error"/>
392 <param name="write_protein_sequence" value="false"/> 425 <param name="write_protein_sequence" value="false"/>
393 <param name="write_protein_description" value="false"/> 426 <param name="write_protein_description" value="false"/>
394 <param name="keep_unreferenced_proteins" value="false"/> 427 <param name="keep_unreferenced_proteins" value="false"/>
395 <param name="unmatched_action" value="remove"/> 428 <param name="unmatched_action" value="remove"/>
396 <param name="aaa_max" value="4"/> 429 <param name="aaa_max" value="4"/>
397 <param name="mismatches_max" value="0"/> 430 <param name="mismatches_max" value="0"/>
398 <param name="IL_equivalent" value="false"/> 431 <param name="IL_equivalent" value="false"/>
399 <section name="enzyme"> 432 <param name="allow_nterm_protein_cleavage" value="true"/>
400 <param name="name" value="auto"/> 433 <section name="enzyme">
401 <param name="specificity" value="none"/> 434 <param name="name" value="auto"/>
402 </section> 435 <param name="specificity" value="none"/>
403 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 436 </section>
404 <output name="ctd_out" ftype="xml"> 437 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
405 <assert_contents> 438 <output name="ctd_out" ftype="xml">
406 <is_valid_xml/> 439 <assert_contents>
407 </assert_contents> 440 <is_valid_xml/>
408 </output> 441 </assert_contents>
442 </output>
443 <assert_stdout>
444 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
445 </assert_stdout>
409 </test> 446 </test>
410 <!-- TOPP_PeptideIndexer_10 --> 447 <!-- TOPP_PeptideIndexer_10 -->
411 <test expect_num_outputs="2"> 448 <test expect_num_outputs="2">
412 <section name="adv_opts"> 449 <section name="adv_opts">
413 <param name="force" value="false"/> 450 <param name="force" value="false"/>
414 <param name="test" value="true"/> 451 <param name="test" value="true"/>
415 </section> 452 </section>
416 <param name="in" value="PeptideIndexer_10_input.idXML"/> 453 <param name="in" value="PeptideIndexer_10_input.idXML"/>
417 <param name="fasta" value="PeptideIndexer_10_input.fasta"/> 454 <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"/> 455 <output name="out" value="PeptideIndexer_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
419 <param name="decoy_string" value=""/> 456 <param name="decoy_string" value=""/>
420 <param name="decoy_string_position" value="prefix"/> 457 <param name="decoy_string_position" value="prefix"/>
421 <param name="missing_decoy_action" value="error"/> 458 <param name="missing_decoy_action" value="error"/>
422 <param name="write_protein_sequence" value="true"/> 459 <param name="write_protein_sequence" value="true"/>
423 <param name="write_protein_description" value="false"/> 460 <param name="write_protein_description" value="false"/>
424 <param name="keep_unreferenced_proteins" value="false"/> 461 <param name="keep_unreferenced_proteins" value="false"/>
425 <param name="unmatched_action" value="error"/> 462 <param name="unmatched_action" value="error"/>
426 <param name="aaa_max" value="3"/> 463 <param name="aaa_max" value="3"/>
427 <param name="mismatches_max" value="0"/> 464 <param name="mismatches_max" value="0"/>
428 <param name="IL_equivalent" value="true"/> 465 <param name="IL_equivalent" value="true"/>
466 <param name="allow_nterm_protein_cleavage" value="true"/>
429 <section name="enzyme"> 467 <section name="enzyme">
430 <param name="name" value="auto"/> 468 <param name="name" value="auto"/>
431 <param name="specificity" value="auto"/> 469 <param name="specificity" value="auto"/>
432 </section> 470 </section>
433 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 471 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
434 <output name="ctd_out" ftype="xml"> 472 <output name="ctd_out" ftype="xml">
435 <assert_contents> 473 <assert_contents>
436 <is_valid_xml/> 474 <is_valid_xml/>
437 </assert_contents> 475 </assert_contents>
438 </output> 476 </output>
477 <assert_stdout>
478 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
479 </assert_stdout>
439 </test> 480 </test>
440 <!-- TOPP_PeptideIndexer_12 --> 481 <!-- TOPP_PeptideIndexer_12 -->
441 <test expect_num_outputs="2"> 482 <test expect_num_outputs="2">
442 <section name="adv_opts"> 483 <section name="adv_opts">
443 <param name="force" value="false"/> 484 <param name="force" value="false"/>
444 <param name="test" value="true"/> 485 <param name="test" value="true"/>
445 </section> 486 </section>
446 <param name="in" value="PeptideIndexer_1.idXML"/> 487 <param name="in" value="PeptideIndexer_1.idXML"/>
447 <param name="fasta" value="PeptideIndexer_1.fasta"/> 488 <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"/> 489 <output name="out" value="PeptideIndexer_12_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
449 <param name="decoy_string" value=""/> 490 <param name="decoy_string" value=""/>
450 <param name="decoy_string_position" value="prefix"/> 491 <param name="decoy_string_position" value="prefix"/>
451 <param name="missing_decoy_action" value="error"/> 492 <param name="missing_decoy_action" value="error"/>
452 <param name="write_protein_sequence" value="false"/> 493 <param name="write_protein_sequence" value="false"/>
453 <param name="write_protein_description" value="false"/> 494 <param name="write_protein_description" value="false"/>
454 <param name="keep_unreferenced_proteins" value="false"/> 495 <param name="keep_unreferenced_proteins" value="false"/>
455 <param name="unmatched_action" value="warn"/> 496 <param name="unmatched_action" value="warn"/>
456 <param name="aaa_max" value="4"/> 497 <param name="aaa_max" value="4"/>
457 <param name="mismatches_max" value="0"/> 498 <param name="mismatches_max" value="0"/>
458 <param name="IL_equivalent" value="false"/> 499 <param name="IL_equivalent" value="false"/>
459 <section name="enzyme"> 500 <param name="allow_nterm_protein_cleavage" value="true"/>
460 <param name="name" value="auto"/> 501 <section name="enzyme">
461 <param name="specificity" value="none"/> 502 <param name="name" value="auto"/>
462 </section> 503 <param name="specificity" value="none"/>
463 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 504 </section>
464 <output name="ctd_out" ftype="xml"> 505 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
465 <assert_contents> 506 <output name="ctd_out" ftype="xml">
466 <is_valid_xml/> 507 <assert_contents>
467 </assert_contents> 508 <is_valid_xml/>
468 </output> 509 </assert_contents>
510 </output>
511 <assert_stdout>
512 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
513 </assert_stdout>
469 </test> 514 </test>
470 <!-- TOPP_PeptideIndexer_13 --> 515 <!-- TOPP_PeptideIndexer_13 -->
471 <test expect_num_outputs="2"> 516 <test expect_num_outputs="2">
472 <section name="adv_opts"> 517 <section name="adv_opts">
473 <param name="force" value="false"/> 518 <param name="force" value="false"/>
474 <param name="test" value="true"/> 519 <param name="test" value="true"/>
475 </section> 520 </section>
476 <param name="in" value="empty.idXML"/> 521 <param name="in" value="empty_0.idXML"/>
477 <param name="fasta" value="PeptideIndexer_1.fasta"/> 522 <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"/> 523 <output name="out" value="empty_1.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
479 <param name="decoy_string" value=""/> 524 <param name="decoy_string" value=""/>
480 <param name="decoy_string_position" value="prefix"/> 525 <param name="decoy_string_position" value="prefix"/>
481 <param name="missing_decoy_action" value="error"/> 526 <param name="missing_decoy_action" value="error"/>
482 <param name="write_protein_sequence" value="false"/> 527 <param name="write_protein_sequence" value="false"/>
483 <param name="write_protein_description" value="false"/> 528 <param name="write_protein_description" value="false"/>
484 <param name="keep_unreferenced_proteins" value="false"/> 529 <param name="keep_unreferenced_proteins" value="false"/>
485 <param name="unmatched_action" value="error"/> 530 <param name="unmatched_action" value="error"/>
486 <param name="aaa_max" value="4"/> 531 <param name="aaa_max" value="4"/>
487 <param name="mismatches_max" value="0"/> 532 <param name="mismatches_max" value="0"/>
488 <param name="IL_equivalent" value="false"/> 533 <param name="IL_equivalent" value="false"/>
534 <param name="allow_nterm_protein_cleavage" value="true"/>
489 <section name="enzyme"> 535 <section name="enzyme">
490 <param name="name" value="auto"/> 536 <param name="name" value="auto"/>
491 <param name="specificity" value="auto"/> 537 <param name="specificity" value="auto"/>
492 </section> 538 </section>
493 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 539 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
494 <output name="ctd_out" ftype="xml"> 540 <output name="ctd_out" ftype="xml">
495 <assert_contents> 541 <assert_contents>
496 <is_valid_xml/> 542 <is_valid_xml/>
497 </assert_contents> 543 </assert_contents>
498 </output> 544 </output>
545 <assert_stdout>
546 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
547 </assert_stdout>
499 </test> 548 </test>
500 <!-- TOPP_PeptideIndexer_14 --> 549 <!-- TOPP_PeptideIndexer_14 -->
501 <test expect_num_outputs="2"> 550 <test expect_num_outputs="2">
502 <section name="adv_opts"> 551 <section name="adv_opts">
503 <param name="force" value="false"/> 552 <param name="force" value="false"/>
504 <param name="test" value="true"/> 553 <param name="test" value="true"/>
505 </section> 554 </section>
506 <param name="in" value="PeptideIndexer_14.idXML"/> 555 <param name="in" value="PeptideIndexer_14.idXML"/>
507 <param name="fasta" value="PeptideIndexer_2.fasta"/> 556 <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"/> 557 <output name="out" value="PeptideIndexer_14_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
509 <param name="decoy_string" value=""/> 558 <param name="decoy_string" value=""/>
510 <param name="decoy_string_position" value="prefix"/> 559 <param name="decoy_string_position" value="prefix"/>
511 <param name="missing_decoy_action" value="error"/> 560 <param name="missing_decoy_action" value="error"/>
512 <param name="write_protein_sequence" value="true"/> 561 <param name="write_protein_sequence" value="true"/>
513 <param name="write_protein_description" value="false"/> 562 <param name="write_protein_description" value="false"/>
514 <param name="keep_unreferenced_proteins" value="false"/> 563 <param name="keep_unreferenced_proteins" value="false"/>
515 <param name="unmatched_action" value="error"/> 564 <param name="unmatched_action" value="error"/>
516 <param name="aaa_max" value="4"/> 565 <param name="aaa_max" value="4"/>
517 <param name="mismatches_max" value="0"/> 566 <param name="mismatches_max" value="0"/>
518 <param name="IL_equivalent" value="false"/> 567 <param name="IL_equivalent" value="false"/>
519 <section name="enzyme"> 568 <param name="allow_nterm_protein_cleavage" value="true"/>
520 <param name="name" value="auto"/> 569 <section name="enzyme">
521 <param name="specificity" value="none"/> 570 <param name="name" value="auto"/>
522 </section> 571 <param name="specificity" value="none"/>
523 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 572 </section>
524 <output name="ctd_out" ftype="xml"> 573 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
525 <assert_contents> 574 <output name="ctd_out" ftype="xml">
526 <is_valid_xml/> 575 <assert_contents>
527 </assert_contents> 576 <is_valid_xml/>
528 </output> 577 </assert_contents>
578 </output>
579 <assert_stdout>
580 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
581 </assert_stdout>
529 </test> 582 </test>
530 </tests> 583 </tests>
531 <help><![CDATA[Refreshes the protein references for all peptide hits. 584 <help><![CDATA[Refreshes the protein references for all peptide hits.
532 585
533 586
534 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PeptideIndexer.html]]></help> 587 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PeptideIndexer.html]]></help>
535 <expand macro="references"/> 588 <expand macro="references"/>
536 </tool> 589 </tool>