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comparison OpenPepXLLF.xml @ 8:8bfa9d787dc7 draft default tip

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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 19:13:01 +0000
parents e574d3f268f6
children
comparison
equal deleted inserted replaced
7:811efed0a9c3 8:8bfa9d787dc7
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: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="OpenPepXLLF" name="OpenPepXLLF" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="OpenPepXLLF" name="OpenPepXLLF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Tool for protein-protein cross linking with label-free linkers.</description> 5 <description>Tool for protein-protein cross linking with label-free linkers.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenPepXLLF</token> 7 <token name="@EXECUTABLE@">OpenPepXLLF</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@
30 mkdir out_xquestxml && 28 mkdir out_xquestxml &&
31 #end if 29 #end if
32 #if "out_xquest_specxml_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 30 #if "out_xquest_specxml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
33 mkdir out_xquest_specxml && 31 mkdir out_xquest_specxml &&
34 #end if 32 #end if
35 #if $adv_opts_cond.adv_opts_selector=='advanced': 33 #if $adv_opts.decoy_database:
36 #if $adv_opts_cond.decoy_database: 34 mkdir adv_opts.decoy_database &&
37 mkdir adv_opts_cond.decoy_database && 35 ln -s '$adv_opts.decoy_database' 'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)' &&
38 ln -s '$adv_opts_cond.decoy_database' 'adv_opts_cond.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts_cond.decoy_database.element_identifier)}.$gxy2omsext($adv_opts_cond.decoy_database.ext)' &&
39 #end if 36 #end if
40 #end if
41 37
42 ## Main program call 38 ## Main program call
43 39
44 set -o pipefail && 40 set -o pipefail &&
45 @EXECUTABLE@ -write_ctd ./ && 41 @EXECUTABLE@ -write_ctd ./ &&
63 #end if 59 #end if
64 #if "out_xquest_specxml_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 60 #if "out_xquest_specxml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
65 -out_xquest_specxml 61 -out_xquest_specxml
66 'out_xquest_specxml/output.${gxy2omsext("spec.xml")}' 62 'out_xquest_specxml/output.${gxy2omsext("spec.xml")}'
67 #end if 63 #end if
68 #if $adv_opts_cond.adv_opts_selector=='advanced': 64 #if $adv_opts.decoy_database:
69 #if $adv_opts_cond.decoy_database:
70 -decoy_database 65 -decoy_database
71 'adv_opts_cond.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts_cond.decoy_database.element_identifier)}.$gxy2omsext($adv_opts_cond.decoy_database.ext)' 66 'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)'
72 #end if 67 #end if
73 #end if
74 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 68 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
75 | tee '$stdout' 69 | tee '$stdout'
76 #end if 70 #end if
77 71
78 ## Postprocessing 72 ## Postprocessing
94 <configfiles> 88 <configfiles>
95 <inputs name="args_json" data_style="paths"/> 89 <inputs name="args_json" data_style="paths"/>
96 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 90 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
97 </configfiles> 91 </configfiles>
98 <inputs> 92 <inputs>
99 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file containing the spectra" help=" select mzml data sets(s)"/> 93 <param argument="-in" type="data" format="mzml" optional="false" label="Input file containing the spectra" help=" select mzml data sets(s)"/>
100 <param name="database" argument="-database" type="data" format="fasta" optional="false" label="Input file containing the protein database" help=" select fasta data sets(s)"/> 94 <param argument="-database" type="data" format="fasta" optional="false" label="Input file containing the protein database" help=" select fasta data sets(s)"/>
101 <param name="decoy_string" argument="-decoy_string" type="text" optional="true" value="DECOY_" label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" help=""> 95 <param argument="-decoy_string" type="text" optional="true" value="DECOY_" label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" help="">
102 <expand macro="list_string_san"/> 96 <expand macro="list_string_san" name="decoy_string"/>
103 </param> 97 </param>
104 <param name="decoy_prefix" argument="-decoy_prefix" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Set to true, if the decoy_string is a prefix of accessions in the protein database" help="Otherwise it is a suffix"/> 98 <param argument="-decoy_prefix" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Set to true, if the decoy_string is a prefix of accessions in the protein database" help="Otherwise it is a suffix"/>
105 <section name="precursor" title="Precursor filtering settings" help="" expanded="false"> 99 <section name="precursor" title="Precursor filtering settings" help="" expanded="false">
106 <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/> 100 <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/>
107 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help=""> 101 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
108 <option value="ppm" selected="true">ppm</option> 102 <option value="ppm" selected="true">ppm</option>
109 <option value="Da">Da</option> 103 <option value="Da">Da</option>
110 <expand macro="list_string_san"/> 104 <expand macro="list_string_san" name="mass_tolerance_unit"/>
111 </param> 105 </param>
112 <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="3" label="Minimum precursor charge to be considered" help=""/> 106 <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/>
113 <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="7" label="Maximum precursor charge to be considered" help=""/> 107 <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="8" label="Maximum precursor charge to be considered" help=""/>
114 <param name="corrections" argument="-precursor:corrections" type="text" optional="true" value="2 1 0" label="Monoisotopic peak correction" help="Matches candidates for possible monoisotopic precursor peaks for experimental mass m and given numbers n at masses (m - n * (C13-C12)). These should be ordered from more extreme to less extreme corrections. Numbers later in the list will be preferred in case of ambiguities (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 108 <param name="corrections" argument="-precursor:corrections" type="text" optional="true" value="4 3 2 1 0" label="Monoisotopic peak correction" help="Matches candidates for possible monoisotopic precursor peaks for experimental mass m and given numbers n at masses (m - n * (C13-C12)). These should be ordered from more extreme to less extreme corrections. Numbers later in the list will be preferred in case of ambiguities (space separated list, in order to allow for spaces in list items surround them by single quotes)">
115 <expand macro="list_integer_valsan"/> 109 <expand macro="list_integer_valsan" name="corrections"/>
116 </param> 110 </param>
117 </section> 111 </section>
118 <section name="fragment" title="Fragment peak matching settings" help="" expanded="false"> 112 <section name="fragment" title="Fragment peak matching settings" help="" expanded="false">
119 <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="20.0" label="Fragment mass tolerance" help=""/> 113 <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="20.0" label="Fragment mass tolerance" help=""/>
120 <param name="mass_tolerance_xlinks" argument="-fragment:mass_tolerance_xlinks" type="float" optional="true" value="20.0" label="Fragment mass tolerance for cross-link ions" help=""/> 114 <param name="mass_tolerance_xlinks" argument="-fragment:mass_tolerance_xlinks" type="float" optional="true" value="20.0" label="Fragment mass tolerance for cross-link ions" help=""/>
121 <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of fragment m" help=""> 115 <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment m" help="">
122 <option value="ppm" selected="true">ppm</option> 116 <option value="ppm" selected="true">ppm</option>
123 <option value="Da">Da</option> 117 <option value="Da">Da</option>
124 <expand macro="list_string_san"/> 118 <expand macro="list_string_san" name="mass_tolerance_unit"/>
125 </param> 119 </param>
126 </section> 120 </section>
127 <section name="modifications" title="Peptide modification settings" help="" expanded="false"> 121 <section name="modifications" title="Peptide modification settings" help="" expanded="false">
128 <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)'"> 122 <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)'">
129 <option value="">default (nothing chosen)</option>
130 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 123 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
131 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 124 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
132 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 125 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
133 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 126 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
134 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 127 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
375 <option value="CAMthiopropanoyl (K)">CAMthiopropanoyl (K)</option> 368 <option value="CAMthiopropanoyl (K)">CAMthiopropanoyl (K)</option>
376 <option value="CAMthiopropanoyl (Protein N-term)">CAMthiopropanoyl (Protein N-term)</option> 369 <option value="CAMthiopropanoyl (Protein N-term)">CAMthiopropanoyl (Protein N-term)</option>
377 <option value="Can-FP-biotin (S)">Can-FP-biotin (S)</option> 370 <option value="Can-FP-biotin (S)">Can-FP-biotin (S)</option>
378 <option value="Can-FP-biotin (T)">Can-FP-biotin (T)</option> 371 <option value="Can-FP-biotin (T)">Can-FP-biotin (T)</option>
379 <option value="Can-FP-biotin (Y)">Can-FP-biotin (Y)</option> 372 <option value="Can-FP-biotin (Y)">Can-FP-biotin (Y)</option>
380 <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option> 373 <option value="Carbamidomethyl (C)" selected="true">Carbamidomethyl (C)</option>
381 <option value="Carbamidomethyl (D)">Carbamidomethyl (D)</option> 374 <option value="Carbamidomethyl (D)">Carbamidomethyl (D)</option>
382 <option value="Carbamidomethyl (E)">Carbamidomethyl (E)</option> 375 <option value="Carbamidomethyl (E)">Carbamidomethyl (E)</option>
383 <option value="Carbamidomethyl (H)">Carbamidomethyl (H)</option> 376 <option value="Carbamidomethyl (H)">Carbamidomethyl (H)</option>
384 <option value="Carbamidomethyl (K)">Carbamidomethyl (K)</option> 377 <option value="Carbamidomethyl (K)">Carbamidomethyl (K)</option>
385 <option value="Carbamidomethyl (M)">Carbamidomethyl (M)</option> 378 <option value="Carbamidomethyl (M)">Carbamidomethyl (M)</option>
1493 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 1486 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
1494 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1487 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1495 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1488 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1496 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1489 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1497 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1490 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1498 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1499 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1491 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1500 <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> 1492 <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>
1501 <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> 1493 <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>
1502 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1494 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1503 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1495 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
3053 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 3045 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
3054 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 3046 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
3055 <option value="ZGB (K)">ZGB (K)</option> 3047 <option value="ZGB (K)">ZGB (K)</option>
3056 <option value="ZGB (N-term)">ZGB (N-term)</option> 3048 <option value="ZGB (N-term)">ZGB (N-term)</option>
3057 <option value="ZQG (K)">ZQG (K)</option> 3049 <option value="ZQG (K)">ZQG (K)</option>
3058 <expand macro="list_string_san"/> 3050 <expand macro="list_string_san" name="fixed"/>
3059 </param> 3051 </param>
3060 <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)'"> 3052 <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)'">
3061 <option value="">default (nothing chosen)</option>
3062 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 3053 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
3063 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 3054 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
3064 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 3055 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
3065 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 3056 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
3066 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 3057 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
4426 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4417 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4427 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4418 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4428 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4419 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
4429 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 4420 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
4430 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 4421 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4431 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4432 <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> 4422 <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>
4433 <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> 4423 <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>
4434 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 4424 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4435 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4425 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
4436 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option> 4426 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
5400 <option value="Oxidation (F)">Oxidation (F)</option> 5390 <option value="Oxidation (F)">Oxidation (F)</option>
5401 <option value="Oxidation (H)">Oxidation (H)</option> 5391 <option value="Oxidation (H)">Oxidation (H)</option>
5402 <option value="Oxidation (I)">Oxidation (I)</option> 5392 <option value="Oxidation (I)">Oxidation (I)</option>
5403 <option value="Oxidation (K)">Oxidation (K)</option> 5393 <option value="Oxidation (K)">Oxidation (K)</option>
5404 <option value="Oxidation (L)">Oxidation (L)</option> 5394 <option value="Oxidation (L)">Oxidation (L)</option>
5405 <option value="Oxidation (M)">Oxidation (M)</option> 5395 <option value="Oxidation (M)" selected="true">Oxidation (M)</option>
5406 <option value="Oxidation (N)">Oxidation (N)</option> 5396 <option value="Oxidation (N)">Oxidation (N)</option>
5407 <option value="Oxidation (P)">Oxidation (P)</option> 5397 <option value="Oxidation (P)">Oxidation (P)</option>
5408 <option value="Oxidation (Q)">Oxidation (Q)</option> 5398 <option value="Oxidation (Q)">Oxidation (Q)</option>
5409 <option value="Oxidation (R)">Oxidation (R)</option> 5399 <option value="Oxidation (R)">Oxidation (R)</option>
5410 <option value="Oxidation (S)">Oxidation (S)</option> 5400 <option value="Oxidation (S)">Oxidation (S)</option>
5985 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 5975 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
5986 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 5976 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
5987 <option value="ZGB (K)">ZGB (K)</option> 5977 <option value="ZGB (K)">ZGB (K)</option>
5988 <option value="ZGB (N-term)">ZGB (N-term)</option> 5978 <option value="ZGB (N-term)">ZGB (N-term)</option>
5989 <option value="ZQG (K)">ZQG (K)</option> 5979 <option value="ZQG (K)">ZQG (K)</option>
5990 <expand macro="list_string_san"/> 5980 <expand macro="list_string_san" name="variable"/>
5991 </param> 5981 </param>
5992 <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=""/> 5982 <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" optional="true" value="3" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
5993 </section> 5983 </section>
5994 <section name="peptide" title="Settings for digesting proteins into peptides" help="" expanded="false"> 5984 <section name="peptide" title="Settings for digesting proteins into peptides" help="" expanded="false">
5995 <param name="min_size" argument="-peptide:min_size" type="integer" optional="true" value="5" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/> 5985 <param name="min_size" argument="-peptide:min_size" type="integer" optional="true" value="5" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
5996 <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" optional="true" value="2" label="Number of missed cleavages" help=""/> 5986 <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" optional="true" value="3" label="Number of missed cleavages" help=""/>
5997 <param name="enzyme" argument="-peptide:enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> 5987 <param name="enzyme" argument="-peptide:enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
5998 <option value="Trypsin" selected="true">Trypsin</option> 5988 <option value="Trypsin" selected="true">Trypsin</option>
5989 <option value="Asp-N">Asp-N</option>
5990 <option value="Asp-N/B">Asp-N/B</option>
5991 <option value="Asp-N_ambic">Asp-N_ambic</option>
5992 <option value="Lys-C/P">Lys-C/P</option>
5993 <option value="PepsinA">PepsinA</option>
5994 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
5995 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
5996 <option value="2-iodobenzoate">2-iodobenzoate</option>
5999 <option value="iodosobenzoate">iodosobenzoate</option> 5997 <option value="iodosobenzoate">iodosobenzoate</option>
6000 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 5998 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
6001 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 5999 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
6002 <option value="Glu-C+P">Glu-C+P</option> 6000 <option value="Glu-C+P">Glu-C+P</option>
6003 <option value="PepsinA + P">PepsinA + P</option> 6001 <option value="PepsinA + P">PepsinA + P</option>
6004 <option value="cyanogen-bromide">cyanogen-bromide</option> 6002 <option value="cyanogen-bromide">cyanogen-bromide</option>
6005 <option value="Clostripain/P">Clostripain/P</option> 6003 <option value="Clostripain/P">Clostripain/P</option>
6006 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> 6004 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
6007 <option value="no cleavage">no cleavage</option> 6005 <option value="Arg-C/P">Arg-C/P</option>
6008 <option value="unspecific cleavage">unspecific cleavage</option> 6006 <option value="TrypChymo">TrypChymo</option>
6009 <option value="Chymotrypsin">Chymotrypsin</option> 6007 <option value="Trypsin/P">Trypsin/P</option>
6010 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
6011 <option value="CNBr">CNBr</option>
6012 <option value="Formic_acid">Formic_acid</option>
6013 <option value="Lys-C">Lys-C</option>
6014 <option value="Lys-N">Lys-N</option>
6015 <option value="V8-DE">V8-DE</option> 6008 <option value="V8-DE">V8-DE</option>
6016 <option value="V8-E">V8-E</option> 6009 <option value="V8-E">V8-E</option>
6017 <option value="leukocyte elastase">leukocyte elastase</option> 6010 <option value="leukocyte elastase">leukocyte elastase</option>
6018 <option value="proline endopeptidase">proline endopeptidase</option> 6011 <option value="proline endopeptidase">proline endopeptidase</option>
6019 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6020 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
6021 <option value="2-iodobenzoate">2-iodobenzoate</option>
6022 <option value="Lys-C/P">Lys-C/P</option>
6023 <option value="PepsinA">PepsinA</option>
6024 <option value="TrypChymo">TrypChymo</option>
6025 <option value="Trypsin/P">Trypsin/P</option>
6026 <option value="Arg-C">Arg-C</option> 6012 <option value="Arg-C">Arg-C</option>
6027 <option value="Arg-C/P">Arg-C/P</option> 6013 <option value="Chymotrypsin">Chymotrypsin</option>
6028 <option value="Asp-N">Asp-N</option> 6014 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
6029 <option value="Asp-N/B">Asp-N/B</option> 6015 <option value="CNBr">CNBr</option>
6030 <option value="Asp-N_ambic">Asp-N_ambic</option> 6016 <option value="no cleavage">no cleavage</option>
6031 <expand macro="list_string_san"/> 6017 <option value="unspecific cleavage">unspecific cleavage</option>
6018 <option value="Formic_acid">Formic_acid</option>
6019 <option value="Lys-C">Lys-C</option>
6020 <option value="Lys-N">Lys-N</option>
6021 <expand macro="list_string_san" name="enzyme"/>
6032 </param> 6022 </param>
6033 </section> 6023 </section>
6034 <section name="cross_linker" title="Description of the cross-linker reagent" help="" expanded="false"> 6024 <section name="cross_linker" title="Description of the cross-linker reagent" help="" expanded="false">
6035 <param name="residue1" argument="-cross_linker:residue1" type="text" optional="true" value="K N-term" label="Comma separated residues, that the first side of a bifunctional cross-linker can attach to" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6025 <param name="residue1" argument="-cross_linker:residue1" type="text" optional="true" value="K N-term" label="Comma separated residues, that the first side of a bifunctional cross-linker can attach to" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6036 <expand macro="list_string_val"/> 6026 <expand macro="list_string_val" name="residue1"/>
6037 <expand macro="list_string_san"/> 6027 <expand macro="list_string_san" name="residue1"/>
6038 </param> 6028 </param>
6039 <param name="residue2" argument="-cross_linker:residue2" type="text" optional="true" value="K N-term" label="Comma separated residues, that the second side of a bifunctional cross-linker can attach to" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6029 <param name="residue2" argument="-cross_linker:residue2" type="text" optional="true" value="K N-term" label="Comma separated residues, that the second side of a bifunctional cross-linker can attach to" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6040 <expand macro="list_string_val"/> 6030 <expand macro="list_string_val" name="residue2"/>
6041 <expand macro="list_string_san"/> 6031 <expand macro="list_string_san" name="residue2"/>
6042 </param> 6032 </param>
6043 <param name="mass" argument="-cross_linker:mass" type="float" optional="true" value="138.0680796" label="Mass of the light cross-linker, linking two residues on one or two peptides" help=""/> 6033 <param name="mass" argument="-cross_linker:mass" type="float" optional="true" value="138.0680796" label="Mass of the light cross-linker, linking two residues on one or two peptides" help=""/>
6044 <param name="mass_mono_link" argument="-cross_linker:mass_mono_link" type="text" optional="true" value="156.07864431 155.094628715" label="Possible masses of the linker, when attached to only one peptide" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6034 <param name="mass_mono_link" argument="-cross_linker:mass_mono_link" type="text" optional="true" value="156.07864431 155.094628715" label="Possible masses of the linker, when attached to only one peptide" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6045 <expand macro="list_float_valsan"/> 6035 <expand macro="list_float_valsan" name="mass_mono_link"/>
6046 </param> 6036 </param>
6047 <param name="name" argument="-cross_linker:name" type="text" optional="true" value="DSS" label="Name of the searched cross-link, used to resolve ambiguity of equal masses" help="(e.g. DSS or BS3)"> 6037 <param name="name" argument="-cross_linker:name" type="text" optional="true" value="DSS" label="Name of the searched cross-link, used to resolve ambiguity of equal masses" help="(e.g. DSS or BS3)">
6048 <expand macro="list_string_san"/> 6038 <expand macro="list_string_san" name="name"/>
6049 </param> 6039 </param>
6050 </section> 6040 </section>
6051 <section name="algorithm" title="Additional algorithm settings" help="" expanded="false"> 6041 <section name="algorithm" title="Additional algorithm settings" help="" expanded="false">
6052 <param name="number_top_hits" argument="-algorithm:number_top_hits" type="integer" optional="true" value="5" label="Number of top hits reported for each spectrum pai" help=""/> 6042 <param name="number_top_hits" argument="-algorithm:number_top_hits" type="integer" optional="true" value="1" label="Number of top hits reported for each spectrum pai" help=""/>
6053 <param name="deisotope" argument="-algorithm:deisotope" display="radio" type="select" optional="false" label="Set to true, if the input spectra should be deisotoped before any other processing steps" help="If set to auto the spectra will be deisotoped, if the fragment mass tolerance is &lt; 0.1 Da or &lt; 100 ppm (0.1 Da at a mass of 1000)"> 6043 <param name="deisotope" argument="-algorithm:deisotope" type="select" optional="true" label="Set to true, if the input spectra should be deisotoped before any other processing steps" help="If set to auto the spectra will be deisotoped, if the fragment mass tolerance is &lt; 0.1 Da or &lt; 100 ppm (0.1 Da at a mass of 1000)">
6054 <option value="true">true</option> 6044 <option value="true">true</option>
6055 <option value="false">false</option> 6045 <option value="false">false</option>
6056 <option value="auto" selected="true">auto</option> 6046 <option value="auto" selected="true">auto</option>
6057 <expand macro="list_string_san"/> 6047 <expand macro="list_string_san" name="deisotope"/>
6058 </param> 6048 </param>
6059 <param name="use_sequence_tags" argument="-algorithm:use_sequence_tags" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use sequence tags (de novo sequencing of short fragments) to filter out candidates before scoring" help="This will make the search faster, but can impact the sensitivity positively or negatively, depending on the dataset"/> 6049 <param name="use_sequence_tags" argument="-algorithm:use_sequence_tags" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use sequence tags (de novo sequencing of short fragments) to filter out candidates before scoring" help="This will make the search faster, but can impact the sensitivity positively or negatively, depending on the dataset"/>
6060 <param name="sequence_tag_min_length" argument="-algorithm:sequence_tag_min_length" type="integer" optional="true" value="2" label="Minimal length of sequence tags to use for filtering candidates" help="Longer tags will make the search faster but much less sensitive. Ignored if 'algorithm:use_sequence_tags' is false"/> 6050 <param name="sequence_tag_min_length" argument="-algorithm:sequence_tag_min_length" type="integer" optional="true" value="2" label="Minimal length of sequence tags to use for filtering candidates" help="Longer tags will make the search faster but much less sensitive. Ignored if 'algorithm:use_sequence_tags' is false"/>
6061 </section> 6051 </section>
6062 <section name="ions" title="Ion types to search for in MS/MS spectra" help="" expanded="false"> 6052 <section name="ions" title="Ion types to search for in MS/MS spectra" help="" expanded="false">
6067 <param name="c_ions" argument="-ions:c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search for peaks of c-ions" help=""/> 6057 <param name="c_ions" argument="-ions:c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search for peaks of c-ions" help=""/>
6068 <param name="z_ions" argument="-ions:z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search for peaks of z-ions" help=""/> 6058 <param name="z_ions" argument="-ions:z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search for peaks of z-ions" help=""/>
6069 <param name="neutral_losses" argument="-ions:neutral_losses" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Search for neutral losses of H2O and H3N" help=""/> 6059 <param name="neutral_losses" argument="-ions:neutral_losses" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Search for neutral losses of H2O and H3N" help=""/>
6070 </section> 6060 </section>
6071 <expand macro="adv_opts_macro"> 6061 <expand macro="adv_opts_macro">
6072 <param name="decoy_database" argument="-decoy_database" type="data" format="fasta" optional="true" label="Input file containing the decoy protein database" help="Decoys can also be included in the normal database file instead (or additionally) select fasta data sets(s)"/> 6062 <param argument="-decoy_database" type="data" format="fasta" optional="true" label="Input file containing the decoy protein database" help="Decoys can also be included in the normal database file instead (or additionally) select fasta data sets(s)"/>
6073 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 6063 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
6074 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 6064 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
6075 <expand macro="list_string_san"/> 6065 <expand macro="list_string_san" name="test"/>
6076 </param> 6066 </param>
6077 </expand> 6067 </expand>
6078 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 6068 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
6079 <option value="out_idXML_FLAG">out_idXML (Results in idXML format (at least one of these output parameters should be set, otherwise you will not have any results))</option> 6069 <option value="out_idXML_FLAG">out_idXML (Results in idXML format (at least one of these output parameters should be set, otherwise you will not have any results))</option>
6080 <option value="out_mzIdentML_FLAG">out_mzIdentML (Results in mzIdentML (.mzid) format (at least one of these output parameters should be set, otherwise you will not have any results))</option> 6070 <option value="out_mzIdentML_FLAG">out_mzIdentML (Results in mzIdentML (.mzid) format (at least one of these output parameters should be set, otherwise you will not have any results))</option>
6101 </data> 6091 </data>
6102 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 6092 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
6103 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 6093 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
6104 </data> 6094 </data>
6105 </outputs> 6095 </outputs>
6106 <tests> 6096 <tests><!-- TOPP_OpenPepXLLF_1 -->
6107 <expand macro="autotest_OpenPepXLLF"/> 6097 <test expect_num_outputs="5">
6108 <expand macro="manutest_OpenPepXLLF"/> 6098 <section name="adv_opts">
6099 <param name="force" value="false"/>
6100 <param name="test" value="true"/>
6101 </section>
6102 <param name="in" value="OpenPepXLLF_input.mzML"/>
6103 <param name="database" value="OpenPepXLLF_input.fasta"/>
6104 <param name="decoy_string" value="decoy"/>
6105 <param name="decoy_prefix" value="true"/>
6106 <output name="out_idXML" file="OpenPepXLLF_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6107 <output name="out_mzIdentML" file="OpenPepXLLF_output.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
6108 <output name="out_xquestxml" file="OpenPepXLLF_output.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
6109 <output name="out_xquest_specxml" file="OpenPepXLLF_output.spec.xml" compare="sim_size" delta_frac="0.7" ftype="spec.xml"/>
6110 <section name="precursor">
6111 <param name="mass_tolerance" value="10.0"/>
6112 <param name="mass_tolerance_unit" value="ppm"/>
6113 <param name="min_charge" value="2"/>
6114 <param name="max_charge" value="8"/>
6115 <param name="corrections" value="4 3 2 1 0"/>
6116 </section>
6117 <section name="fragment">
6118 <param name="mass_tolerance" value="20.0"/>
6119 <param name="mass_tolerance_xlinks" value="20.0"/>
6120 <param name="mass_tolerance_unit" value="ppm"/>
6121 </section>
6122 <section name="modifications">
6123 <param name="fixed" value="Carbamidomethyl (C)"/>
6124 <param name="variable" value="Oxidation (M)"/>
6125 <param name="variable_max_per_peptide" value="3"/>
6126 </section>
6127 <section name="peptide">
6128 <param name="min_size" value="5"/>
6129 <param name="missed_cleavages" value="3"/>
6130 <param name="enzyme" value="Trypsin"/>
6131 </section>
6132 <section name="cross_linker">
6133 <param name="residue1" value="&quot;K&quot; &quot;N-term&quot;"/>
6134 <param name="residue2" value="&quot;K&quot; &quot;N-term&quot;"/>
6135 <param name="mass" value="138.0680796"/>
6136 <param name="mass_mono_link" value="156.07864431 155.094628715"/>
6137 <param name="name" value="DSS"/>
6138 </section>
6139 <section name="algorithm">
6140 <param name="number_top_hits" value="1"/>
6141 <param name="deisotope" value="auto"/>
6142 <param name="use_sequence_tags" value="false"/>
6143 <param name="sequence_tag_min_length" value="2"/>
6144 </section>
6145 <section name="ions">
6146 <param name="b_ions" value="true"/>
6147 <param name="y_ions" value="true"/>
6148 <param name="a_ions" value="false"/>
6149 <param name="x_ions" value="false"/>
6150 <param name="c_ions" value="false"/>
6151 <param name="z_ions" value="false"/>
6152 <param name="neutral_losses" value="true"/>
6153 </section>
6154 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/>
6155 <output name="ctd_out" ftype="xml">
6156 <assert_contents>
6157 <is_valid_xml/>
6158 </assert_contents>
6159 </output>
6160 </test>
6161 <!-- TOPP_OpenPepXLLF_2 -->
6162 <test expect_num_outputs="2">
6163 <section name="adv_opts">
6164 <param name="force" value="false"/>
6165 <param name="test" value="true"/>
6166 </section>
6167 <param name="in" value="OpenPepXLLF_input2.mzML"/>
6168 <param name="database" value="OpenPepXLLF_input2.fasta"/>
6169 <param name="decoy_string" value="decoy_"/>
6170 <param name="decoy_prefix" value="true"/>
6171 <output name="out_idXML" file="OpenPepXLLF_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6172 <section name="precursor">
6173 <param name="mass_tolerance" value="10.0"/>
6174 <param name="mass_tolerance_unit" value="ppm"/>
6175 <param name="min_charge" value="3"/>
6176 <param name="max_charge" value="7"/>
6177 <param name="corrections" value="1 0"/>
6178 </section>
6179 <section name="fragment">
6180 <param name="mass_tolerance" value="0.2"/>
6181 <param name="mass_tolerance_xlinks" value="0.3"/>
6182 <param name="mass_tolerance_unit" value="Da"/>
6183 </section>
6184 <section name="modifications">
6185 <param name="fixed" value="Carbamidomethyl (C)"/>
6186 <param name="variable" value="Oxidation (M)"/>
6187 <param name="variable_max_per_peptide" value="1"/>
6188 </section>
6189 <section name="peptide">
6190 <param name="min_size" value="5"/>
6191 <param name="missed_cleavages" value="1"/>
6192 <param name="enzyme" value="Trypsin"/>
6193 </section>
6194 <section name="cross_linker">
6195 <param name="residue1" value="&quot;D&quot; &quot;E&quot; &quot;C-term&quot;"/>
6196 <param name="residue2" value="&quot;K&quot; &quot;S&quot; &quot;T&quot; &quot;Y&quot; &quot;N-term&quot;"/>
6197 <param name="mass" value="-18.010595"/>
6198 <param name="mass_mono_link" value=""/>
6199 <param name="name" value="DMTMM"/>
6200 </section>
6201 <section name="algorithm">
6202 <param name="number_top_hits" value="1"/>
6203 <param name="deisotope" value="auto"/>
6204 <param name="use_sequence_tags" value="false"/>
6205 <param name="sequence_tag_min_length" value="2"/>
6206 </section>
6207 <section name="ions">
6208 <param name="b_ions" value="true"/>
6209 <param name="y_ions" value="true"/>
6210 <param name="a_ions" value="false"/>
6211 <param name="x_ions" value="false"/>
6212 <param name="c_ions" value="false"/>
6213 <param name="z_ions" value="false"/>
6214 <param name="neutral_losses" value="true"/>
6215 </section>
6216 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/>
6217 <output name="ctd_out" ftype="xml">
6218 <assert_contents>
6219 <is_valid_xml/>
6220 </assert_contents>
6221 </output>
6222 </test>
6109 </tests> 6223 </tests>
6110 <help><![CDATA[Tool for protein-protein cross linking with label-free linkers. 6224 <help><![CDATA[Tool for protein-protein cross linking with label-free linkers.
6111 6225
6112 6226
6113 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenPepXLLF.html]]></help> 6227 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenPepXLLF.html]]></help>
6114 <expand macro="references"/> 6228 <expand macro="references"/>
6115 </tool> 6229 </tool>