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comparison RNPxlSearch.xml @ 11:0f97ea098da0 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 19:19:49 +0000
parents 3dc6d9795d5b
children 33e2670c3a18
comparison
equal deleted inserted replaced
10:7df285ee982e 11:0f97ea098da0
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="RNPxlSearch" name="RNPxlSearch" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="RNPxlSearch" name="RNPxlSearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Annotate RNA/DNA-peptide cross-links in MS/MS spectra.</description> 5 <description>Annotate RNA/DNA-peptide cross-links in MS/MS spectra.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">RNPxlSearch</token> 7 <token name="@EXECUTABLE@">RNPxlSearch</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@
56 <configfiles> 54 <configfiles>
57 <inputs name="args_json" data_style="paths"/> 55 <inputs name="args_json" data_style="paths"/>
58 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
59 </configfiles> 57 </configfiles>
60 <inputs> 58 <inputs>
61 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> 59 <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
62 <param name="database" argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/> 60 <param argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
63 <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false"> 61 <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
64 <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance (+/- around precursor m/z)" help=""/> 62 <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance (+/- around precursor m/z)" help=""/>
65 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help=""> 63 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
66 <option value="ppm" selected="true">ppm</option> 64 <option value="ppm" selected="true">ppm</option>
67 <option value="Da">Da</option> 65 <option value="Da">Da</option>
68 <expand macro="list_string_san"/> 66 <expand macro="list_string_san" name="mass_tolerance_unit"/>
69 </param> 67 </param>
70 <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/> 68 <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/>
71 <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/> 69 <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/>
72 <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 70 <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
73 <expand macro="list_integer_valsan"/> 71 <expand macro="list_integer_valsan" name="isotopes"/>
74 </param> 72 </param>
75 </section> 73 </section>
76 <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false"> 74 <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false">
77 <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/> 75 <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/>
78 <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of fragment m" help=""> 76 <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment m" help="">
79 <option value="ppm" selected="true">ppm</option> 77 <option value="ppm" selected="true">ppm</option>
80 <option value="Da">Da</option> 78 <option value="Da">Da</option>
81 <expand macro="list_string_san"/> 79 <expand macro="list_string_san" name="mass_tolerance_unit"/>
82 </param> 80 </param>
83 </section> 81 </section>
84 <section name="modifications" title="Modifications Options" help="" expanded="false"> 82 <section name="modifications" title="Modifications Options" help="" expanded="false">
85 <param name="fixed" argument="-modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'"> 83 <param name="fixed" argument="-modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
86 <option value="">default (nothing chosen)</option>
87 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 84 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
88 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 85 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
89 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 86 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
90 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 87 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
91 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 88 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
1450 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 1447 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
1451 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1448 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1452 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1449 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1453 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1450 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1454 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1451 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1455 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1456 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1452 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1457 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option> 1453 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
1458 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> 1454 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
1459 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1455 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1460 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1456 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
3010 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 3006 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
3011 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 3007 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
3012 <option value="ZGB (K)">ZGB (K)</option> 3008 <option value="ZGB (K)">ZGB (K)</option>
3013 <option value="ZGB (N-term)">ZGB (N-term)</option> 3009 <option value="ZGB (N-term)">ZGB (N-term)</option>
3014 <option value="ZQG (K)">ZQG (K)</option> 3010 <option value="ZQG (K)">ZQG (K)</option>
3015 <expand macro="list_string_san"/> 3011 <expand macro="list_string_san" name="fixed"/>
3016 </param> 3012 </param>
3017 <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'"> 3013 <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
3018 <option value="">default (nothing chosen)</option>
3019 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 3014 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
3020 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 3015 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
3021 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 3016 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
3022 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 3017 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
3023 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 3018 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
4382 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 4377 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
4383 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4378 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4384 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4379 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4385 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4380 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
4386 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 4381 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
4387 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4388 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 4382 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4389 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option> 4383 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
4390 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> 4384 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
4391 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 4385 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4392 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4386 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
5942 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 5936 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
5943 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 5937 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
5944 <option value="ZGB (K)">ZGB (K)</option> 5938 <option value="ZGB (K)">ZGB (K)</option>
5945 <option value="ZGB (N-term)">ZGB (N-term)</option> 5939 <option value="ZGB (N-term)">ZGB (N-term)</option>
5946 <option value="ZQG (K)">ZQG (K)</option> 5940 <option value="ZQG (K)">ZQG (K)</option>
5947 <expand macro="list_string_san"/> 5941 <expand macro="list_string_san" name="variable"/>
5948 </param> 5942 </param>
5949 <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/> 5943 <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
5950 </section> 5944 </section>
5951 <section name="peptide" title="Peptide Options" help="" expanded="false"> 5945 <section name="peptide" title="Peptide Options" help="" expanded="false">
5952 <param name="min_size" argument="-peptide:min_size" type="integer" optional="true" value="6" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/> 5946 <param name="min_size" argument="-peptide:min_size" type="integer" optional="true" value="6" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
5953 <param name="max_size" argument="-peptide:max_size" type="integer" optional="true" value="1000000" label="Maximum size a peptide may have after digestion to be considered in the search" help=""/> 5947 <param name="max_size" argument="-peptide:max_size" type="integer" optional="true" value="1000000" label="Maximum size a peptide may have after digestion to be considered in the search" help=""/>
5954 <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/> 5948 <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/>
5955 <param name="enzyme" argument="-peptide:enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> 5949 <param name="enzyme" argument="-peptide:enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
5950 <option value="PepsinA">PepsinA</option>
5951 <option value="TrypChymo">TrypChymo</option>
5952 <option value="Trypsin/P">Trypsin/P</option>
5953 <option value="Trypsin" selected="true">Trypsin</option>
5954 <option value="Lys-N">Lys-N</option>
5955 <option value="Lys-C/P">Lys-C/P</option>
5956 <option value="Clostripain/P">Clostripain/P</option>
5957 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
5958 <option value="no cleavage">no cleavage</option>
5959 <option value="unspecific cleavage">unspecific cleavage</option>
5960 <option value="Arg-C/P">Arg-C/P</option>
5956 <option value="Asp-N">Asp-N</option> 5961 <option value="Asp-N">Asp-N</option>
5957 <option value="Asp-N/B">Asp-N/B</option> 5962 <option value="Asp-N/B">Asp-N/B</option>
5958 <option value="Asp-N_ambic">Asp-N_ambic</option>
5959 <option value="Trypsin" selected="true">Trypsin</option>
5960 <option value="proline endopeptidase">proline endopeptidase</option>
5961 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
5962 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
5963 <option value="2-iodobenzoate">2-iodobenzoate</option>
5964 <option value="iodosobenzoate">iodosobenzoate</option>
5965 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 5963 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
5966 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 5964 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
5967 <option value="Glu-C+P">Glu-C+P</option> 5965 <option value="Glu-C+P">Glu-C+P</option>
5968 <option value="PepsinA + P">PepsinA + P</option> 5966 <option value="PepsinA + P">PepsinA + P</option>
5969 <option value="cyanogen-bromide">cyanogen-bromide</option> 5967 <option value="cyanogen-bromide">cyanogen-bromide</option>
5970 <option value="Clostripain/P">Clostripain/P</option> 5968 <option value="Asp-N_ambic">Asp-N_ambic</option>
5971 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
5972 <option value="no cleavage">no cleavage</option>
5973 <option value="Chymotrypsin">Chymotrypsin</option> 5969 <option value="Chymotrypsin">Chymotrypsin</option>
5974 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 5970 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
5971 <option value="Arg-C">Arg-C</option>
5972 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
5973 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
5974 <option value="2-iodobenzoate">2-iodobenzoate</option>
5975 <option value="iodosobenzoate">iodosobenzoate</option>
5975 <option value="CNBr">CNBr</option> 5976 <option value="CNBr">CNBr</option>
5976 <option value="Lys-C/P">Lys-C/P</option>
5977 <option value="PepsinA">PepsinA</option>
5978 <option value="TrypChymo">TrypChymo</option>
5979 <option value="unspecific cleavage">unspecific cleavage</option>
5980 <option value="Arg-C">Arg-C</option>
5981 <option value="Arg-C/P">Arg-C/P</option>
5982 <option value="Formic_acid">Formic_acid</option> 5977 <option value="Formic_acid">Formic_acid</option>
5983 <option value="Lys-C">Lys-C</option> 5978 <option value="Lys-C">Lys-C</option>
5984 <option value="Lys-N">Lys-N</option>
5985 <option value="Trypsin/P">Trypsin/P</option>
5986 <option value="V8-DE">V8-DE</option> 5979 <option value="V8-DE">V8-DE</option>
5987 <option value="V8-E">V8-E</option> 5980 <option value="V8-E">V8-E</option>
5988 <option value="leukocyte elastase">leukocyte elastase</option> 5981 <option value="leukocyte elastase">leukocyte elastase</option>
5989 <expand macro="list_string_san"/> 5982 <option value="proline endopeptidase">proline endopeptidase</option>
5983 <expand macro="list_string_san" name="enzyme"/>
5990 </param> 5984 </param>
5991 </section> 5985 </section>
5992 <section name="report" title="Reporting Options" help="" expanded="false"> 5986 <section name="report" title="Reporting Options" help="" expanded="false">
5993 <param name="top_hits" argument="-report:top_hits" type="integer" optional="true" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/> 5987 <param name="top_hits" argument="-report:top_hits" type="integer" optional="true" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/>
5994 </section> 5988 </section>
5995 <section name="RNPxl" title="RNPxl Options" help="" expanded="false"> 5989 <section name="RNPxl" title="RNPxl Options" help="" expanded="false">
5996 <param name="length" argument="-RNPxl:length" type="integer" optional="true" value="2" label="Oligonucleotide maximum length" help="0 = disable search for RNA variants"/> 5990 <param name="length" argument="-RNPxl:length" type="integer" optional="true" value="2" label="Oligonucleotide maximum length" help="0 = disable search for RNA variants"/>
5997 <param name="sequence" argument="-RNPxl:sequence" type="text" optional="true" value="" label="Sequence to restrict the generation of oligonucleotide chains" help="(disabled for empty sequence)"> 5991 <param name="sequence" argument="-RNPxl:sequence" type="text" optional="true" value="" label="Sequence to restrict the generation of oligonucleotide chains" help="(disabled for empty sequence)">
5998 <expand macro="list_string_san"/> 5992 <expand macro="list_string_san" name="sequence"/>
5999 </param> 5993 </param>
6000 <param name="target_nucleotides" argument="-RNPxl:target_nucleotides" type="text" optional="true" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format: target nucleotide=empirical formula of nucleoside monophosphate" help="e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU . or e.g. Y=C10H14N5O7PS where Y represents tG (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 5994 <param name="target_nucleotides" argument="-RNPxl:target_nucleotides" type="text" optional="true" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format: target nucleotide=empirical formula of nucleoside monophosphate" help="e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU . or e.g. Y=C10H14N5O7PS where Y represents tG (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6001 <expand macro="list_string_val"/> 5995 <expand macro="list_string_val" name="target_nucleotides"/>
6002 <expand macro="list_string_san"/> 5996 <expand macro="list_string_san" name="target_nucleotides"/>
6003 </param> 5997 </param>
6004 <param name="nt_groups" argument="-RNPxl:nt_groups" type="text" optional="true" value="" label="Restrict which nucleotides can cooccur in a precursor adduct to be able to search both RNA and DNA (Formate" help="e.g.: AU CG) (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 5998 <param name="nt_groups" argument="-RNPxl:nt_groups" type="text" optional="true" value="" label="Restrict which nucleotides can cooccur in a precursor adduct to be able to search both RNA and DNA (Formate" help="e.g.: AU CG) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6005 <expand macro="list_string_val"/> 5999 <expand macro="list_string_val" name="nt_groups"/>
6006 <expand macro="list_string_san"/> 6000 <expand macro="list_string_san" name="nt_groups"/>
6007 </param> 6001 </param>
6008 <param name="mapping" argument="-RNPxl:mapping" type="text" optional="true" value="A-&gt;A C-&gt;C G-&gt;G U-&gt;U" label="format: source-&gt;target e.g. A-&gt;A, ..., U-&gt;U, U-&gt;X" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6002 <param name="mapping" argument="-RNPxl:mapping" type="text" optional="true" value="A-&gt;A C-&gt;C G-&gt;G U-&gt;U" label="format: source-&gt;target e.g. A-&gt;A, ..., U-&gt;U, U-&gt;X" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6009 <expand macro="list_string_val"/> 6003 <expand macro="list_string_val" name="mapping"/>
6010 <expand macro="list_string_san"/> 6004 <expand macro="list_string_san" name="mapping"/>
6011 </param> 6005 </param>
6012 <param name="can_cross_link" argument="-RNPxl:can_cross_link" type="text" optional="true" value="U" label="format: 'U' if only U forms cross-links" help="'CATG' if C, A, G, and T form cross-links"> 6006 <param name="can_cross_link" argument="-RNPxl:can_cross_link" type="text" optional="true" value="U" label="format: 'U' if only U forms cross-links" help="'CATG' if C, A, G, and T form cross-links">
6013 <expand macro="list_string_san"/> 6007 <expand macro="list_string_san" name="can_cross_link"/>
6014 </param> 6008 </param>
6015 <param name="fragment_adducts" argument="-RNPxl:fragment_adducts" type="text" optional="true" value="U:C9H10N2O5;U-H3PO4 U:C4H4N2O2;U' U:C4H2N2O1;U'-H2O U:C3O;C3O U:C9H13N2O9P1;U U:C9H11N2O8P1;U-H2O U:C9H12N2O6;U-HPO3" label="format: [target nucleotide]:[formula] or [precursor adduct]-&gt;[fragment adduct formula];[name]:" help="e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O-&gt;C9H11N2O8P1;U-H2O', (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6009 <param name="fragment_adducts" argument="-RNPxl:fragment_adducts" type="text" optional="true" value="U:C9H10N2O5;U-H3PO4 U:C4H4N2O2;U' U:C4H2N2O1;U'-H2O U:C3O;C3O U:C9H13N2O9P1;U U:C9H11N2O8P1;U-H2O U:C9H12N2O6;U-HPO3" label="format: [target nucleotide]:[formula] or [precursor adduct]-&gt;[fragment adduct formula];[name]:" help="e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O-&gt;C9H11N2O8P1;U-H2O', (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6016 <expand macro="list_string_val"/> 6010 <expand macro="list_string_val" name="fragment_adducts"/>
6017 <expand macro="list_string_san"/> 6011 <expand macro="list_string_san" name="fragment_adducts"/>
6018 </param> 6012 </param>
6019 <param name="modifications" argument="-RNPxl:modifications" type="text" optional="true" value="U: U:-H2O U:-H2O-HPO3 U:-HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6013 <param name="modifications" argument="-RNPxl:modifications" type="text" optional="true" value="U: U:-H2O U:-H2O-HPO3 U:-HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6020 <expand macro="list_string_val"/> 6014 <expand macro="list_string_val" name="modifications"/>
6021 <expand macro="list_string_san"/> 6015 <expand macro="list_string_san" name="modifications"/>
6022 </param> 6016 </param>
6023 <param name="scoring" argument="-RNPxl:scoring" display="radio" type="select" optional="false" label="Scoring algorithm used in prescoring (fast: total-loss, slow: all losses)" help=""> 6017 <param name="scoring" argument="-RNPxl:scoring" type="select" optional="true" label="Scoring algorithm used in prescoring (fast: total-loss, slow: all losses)" help="">
6024 <option value="fast" selected="true">fast</option> 6018 <option value="fast" selected="true">fast</option>
6025 <option value="slow">slow</option> 6019 <option value="slow">slow</option>
6026 <expand macro="list_string_san"/> 6020 <expand macro="list_string_san" name="scoring"/>
6027 </param> 6021 </param>
6028 <param name="decoys" argument="-RNPxl:decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate decoy sequences and spectra" help=""/> 6022 <param name="decoys" argument="-RNPxl:decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate decoy sequences and spectra" help=""/>
6029 <param name="CysteineAdduct" argument="-RNPxl:CysteineAdduct" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if the +152 adduct is expected" help=""/> 6023 <param name="CysteineAdduct" argument="-RNPxl:CysteineAdduct" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if the +152 adduct is expected" help=""/>
6030 <param name="filter_fractional_mass" argument="-RNPxl:filter_fractional_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag to filter non-crosslinks by fractional mass" help=""/> 6024 <param name="filter_fractional_mass" argument="-RNPxl:filter_fractional_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag to filter non-crosslinks by fractional mass" help=""/>
6031 <param name="carbon_labeled_fragments" argument="-RNPxl:carbon_labeled_fragments" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate fragment shifts assuming full labeling of carbon" help="(e.g. completely labeled U13)"/> 6025 <param name="carbon_labeled_fragments" argument="-RNPxl:carbon_labeled_fragments" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate fragment shifts assuming full labeling of carbon" help="(e.g. completely labeled U13)"/>
6032 <param name="only_xl" argument="-RNPxl:only_xl" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only search cross-links and ignore non-cross-linked peptides" help=""/> 6026 <param name="only_xl" argument="-RNPxl:only_xl" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only search cross-links and ignore non-cross-linked peptides" help=""/>
6033 <param name="filter_small_peptide_mass" argument="-RNPxl:filter_small_peptide_mass" type="float" optional="true" value="600.0" label="Filter precursor that can only correspond to non-crosslinks by mass" help=""/> 6027 <param name="filter_small_peptide_mass" argument="-RNPxl:filter_small_peptide_mass" type="float" optional="true" value="600.0" label="Filter precursor that can only correspond to non-crosslinks by mass" help=""/>
6034 <param name="marker_ions_tolerance" argument="-RNPxl:marker_ions_tolerance" type="float" optional="true" value="0.05" label="Tolerance used to determine marker ions (Da)" help=""/> 6028 <param name="marker_ions_tolerance" argument="-RNPxl:marker_ions_tolerance" type="float" optional="true" value="0.05" label="Tolerance used to determine marker ions (Da)" help=""/>
6035 </section> 6029 </section>
6036 <expand macro="adv_opts_macro"> 6030 <expand macro="adv_opts_macro">
6037 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 6031 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
6038 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 6032 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
6039 <expand macro="list_string_san"/> 6033 <expand macro="list_string_san" name="test"/>
6040 </param> 6034 </param>
6041 </expand> 6035 </expand>
6042 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 6036 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
6043 <option value="out_tsv_FLAG">out_tsv (tsv output file)</option> 6037 <option value="out_tsv_FLAG">out_tsv (tsv output file)</option>
6044 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 6038 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
6051 </data> 6045 </data>
6052 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 6046 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
6053 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 6047 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
6054 </data> 6048 </data>
6055 </outputs> 6049 </outputs>
6056 <tests> 6050 <tests><!-- TOPP_RNPxlSearch_1 -->
6057 <expand macro="autotest_RNPxlSearch"/> 6051 <test expect_num_outputs="2">
6058 <expand macro="manutest_RNPxlSearch"/> 6052 <section name="adv_opts">
6053 <param name="force" value="false"/>
6054 <param name="test" value="true"/>
6055 </section>
6056 <param name="in" value="RNPxlSearch_1_input.mzML"/>
6057 <param name="database" value="RNPxlSearch_1_input.fasta"/>
6058 <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6059 <section name="precursor">
6060 <param name="mass_tolerance" value="20.0"/>
6061 <param name="mass_tolerance_unit" value="ppm"/>
6062 <param name="min_charge" value="2"/>
6063 <param name="max_charge" value="5"/>
6064 <param name="isotopes" value="0 1"/>
6065 </section>
6066 <section name="fragment">
6067 <param name="mass_tolerance" value="20.0"/>
6068 <param name="mass_tolerance_unit" value="ppm"/>
6069 </section>
6070 <section name="modifications">
6071 <param name="fixed"/>
6072 <param name="variable" value="Oxidation (M)"/>
6073 <param name="variable_max_per_peptide" value="2"/>
6074 </section>
6075 <section name="peptide">
6076 <param name="min_size" value="6"/>
6077 <param name="max_size" value="1000000"/>
6078 <param name="missed_cleavages" value="1"/>
6079 <param name="enzyme" value="Trypsin"/>
6080 </section>
6081 <section name="report">
6082 <param name="top_hits" value="1"/>
6083 </section>
6084 <section name="RNPxl">
6085 <param name="length" value="2"/>
6086 <param name="sequence" value="GUA"/>
6087 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
6088 <param name="nt_groups" value=""/>
6089 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
6090 <param name="can_cross_link" value="U"/>
6091 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
6092 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
6093 <param name="scoring" value="fast"/>
6094 <param name="decoys" value="false"/>
6095 <param name="CysteineAdduct" value="false"/>
6096 <param name="filter_fractional_mass" value="false"/>
6097 <param name="carbon_labeled_fragments" value="false"/>
6098 <param name="only_xl" value="false"/>
6099 <param name="filter_small_peptide_mass" value="600.0"/>
6100 <param name="marker_ions_tolerance" value="0.05"/>
6101 </section>
6102 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6103 <output name="ctd_out" ftype="xml">
6104 <assert_contents>
6105 <is_valid_xml/>
6106 </assert_contents>
6107 </output>
6108 </test>
6109 <!-- TOPP_RNPxlSearch_2 -->
6110 <test expect_num_outputs="2">
6111 <section name="adv_opts">
6112 <param name="force" value="false"/>
6113 <param name="test" value="true"/>
6114 </section>
6115 <param name="in" value="RNPxlSearch_1_input.mzML"/>
6116 <param name="database" value="RNPxlSearch_1_input.fasta"/>
6117 <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6118 <section name="precursor">
6119 <param name="mass_tolerance" value="20.0"/>
6120 <param name="mass_tolerance_unit" value="ppm"/>
6121 <param name="min_charge" value="2"/>
6122 <param name="max_charge" value="5"/>
6123 <param name="isotopes" value="0 1"/>
6124 </section>
6125 <section name="fragment">
6126 <param name="mass_tolerance" value="20.0"/>
6127 <param name="mass_tolerance_unit" value="ppm"/>
6128 </section>
6129 <section name="modifications">
6130 <param name="fixed"/>
6131 <param name="variable" value="Oxidation (M)"/>
6132 <param name="variable_max_per_peptide" value="2"/>
6133 </section>
6134 <section name="peptide">
6135 <param name="min_size" value="6"/>
6136 <param name="max_size" value="1000000"/>
6137 <param name="missed_cleavages" value="1"/>
6138 <param name="enzyme" value="Trypsin"/>
6139 </section>
6140 <section name="report">
6141 <param name="top_hits" value="1"/>
6142 </section>
6143 <section name="RNPxl">
6144 <param name="length" value="2"/>
6145 <param name="sequence" value="GUA"/>
6146 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
6147 <param name="nt_groups" value=""/>
6148 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
6149 <param name="can_cross_link" value="U"/>
6150 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
6151 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
6152 <param name="scoring" value="fast"/>
6153 <param name="decoys" value="true"/>
6154 <param name="CysteineAdduct" value="false"/>
6155 <param name="filter_fractional_mass" value="false"/>
6156 <param name="carbon_labeled_fragments" value="false"/>
6157 <param name="only_xl" value="false"/>
6158 <param name="filter_small_peptide_mass" value="600.0"/>
6159 <param name="marker_ions_tolerance" value="0.05"/>
6160 </section>
6161 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6162 <output name="ctd_out" ftype="xml">
6163 <assert_contents>
6164 <is_valid_xml/>
6165 </assert_contents>
6166 </output>
6167 </test>
6168 <!-- TOPP_RNPxlSearch_3 -->
6169 <test expect_num_outputs="3">
6170 <section name="adv_opts">
6171 <param name="force" value="false"/>
6172 <param name="test" value="true"/>
6173 </section>
6174 <param name="in" value="RNPxlSearch_1_input.mzML"/>
6175 <param name="database" value="RNPxlSearch_1_input.fasta"/>
6176 <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6177 <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
6178 <section name="precursor">
6179 <param name="mass_tolerance" value="10.0"/>
6180 <param name="mass_tolerance_unit" value="ppm"/>
6181 <param name="min_charge" value="2"/>
6182 <param name="max_charge" value="5"/>
6183 <param name="isotopes" value="0 1"/>
6184 </section>
6185 <section name="fragment">
6186 <param name="mass_tolerance" value="10.0"/>
6187 <param name="mass_tolerance_unit" value="ppm"/>
6188 </section>
6189 <section name="modifications">
6190 <param name="fixed"/>
6191 <param name="variable"/>
6192 <param name="variable_max_per_peptide" value="2"/>
6193 </section>
6194 <section name="peptide">
6195 <param name="min_size" value="6"/>
6196 <param name="max_size" value="1000000"/>
6197 <param name="missed_cleavages" value="1"/>
6198 <param name="enzyme" value="Trypsin"/>
6199 </section>
6200 <section name="report">
6201 <param name="top_hits" value="3"/>
6202 </section>
6203 <section name="RNPxl">
6204 <param name="length" value="2"/>
6205 <param name="sequence" value=""/>
6206 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
6207 <param name="nt_groups" value=""/>
6208 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
6209 <param name="can_cross_link" value="U"/>
6210 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
6211 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
6212 <param name="scoring" value="fast"/>
6213 <param name="decoys" value="false"/>
6214 <param name="CysteineAdduct" value="false"/>
6215 <param name="filter_fractional_mass" value="false"/>
6216 <param name="carbon_labeled_fragments" value="false"/>
6217 <param name="only_xl" value="false"/>
6218 <param name="filter_small_peptide_mass" value="600.0"/>
6219 <param name="marker_ions_tolerance" value="0.05"/>
6220 </section>
6221 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/>
6222 <output name="ctd_out" ftype="xml">
6223 <assert_contents>
6224 <is_valid_xml/>
6225 </assert_contents>
6226 </output>
6227 </test>
6228 <!-- TOPP_RNPxlSearch_4 -->
6229 <test expect_num_outputs="3">
6230 <section name="adv_opts">
6231 <param name="force" value="false"/>
6232 <param name="test" value="true"/>
6233 </section>
6234 <param name="in" value="RNPxlSearch_1_input.mzML"/>
6235 <param name="database" value="RNPxlSearch_1_input.fasta"/>
6236 <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6237 <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
6238 <section name="precursor">
6239 <param name="mass_tolerance" value="10.0"/>
6240 <param name="mass_tolerance_unit" value="ppm"/>
6241 <param name="min_charge" value="2"/>
6242 <param name="max_charge" value="5"/>
6243 <param name="isotopes" value="0 1"/>
6244 </section>
6245 <section name="fragment">
6246 <param name="mass_tolerance" value="10.0"/>
6247 <param name="mass_tolerance_unit" value="ppm"/>
6248 </section>
6249 <section name="modifications">
6250 <param name="fixed"/>
6251 <param name="variable"/>
6252 <param name="variable_max_per_peptide" value="2"/>
6253 </section>
6254 <section name="peptide">
6255 <param name="min_size" value="6"/>
6256 <param name="max_size" value="1000000"/>
6257 <param name="missed_cleavages" value="1"/>
6258 <param name="enzyme" value="Trypsin"/>
6259 </section>
6260 <section name="report">
6261 <param name="top_hits" value="2"/>
6262 </section>
6263 <section name="RNPxl">
6264 <param name="length" value="2"/>
6265 <param name="sequence" value=""/>
6266 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
6267 <param name="nt_groups" value=""/>
6268 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
6269 <param name="can_cross_link" value="U"/>
6270 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
6271 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
6272 <param name="scoring" value="fast"/>
6273 <param name="decoys" value="true"/>
6274 <param name="CysteineAdduct" value="false"/>
6275 <param name="filter_fractional_mass" value="false"/>
6276 <param name="carbon_labeled_fragments" value="false"/>
6277 <param name="only_xl" value="false"/>
6278 <param name="filter_small_peptide_mass" value="600.0"/>
6279 <param name="marker_ions_tolerance" value="0.05"/>
6280 </section>
6281 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/>
6282 <output name="ctd_out" ftype="xml">
6283 <assert_contents>
6284 <is_valid_xml/>
6285 </assert_contents>
6286 </output>
6287 </test>
6059 </tests> 6288 </tests>
6060 <help><![CDATA[Annotate RNA/DNA-peptide cross-links in MS/MS spectra. 6289 <help><![CDATA[Annotate RNA/DNA-peptide cross-links in MS/MS spectra.
6061 6290
6062 6291
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