Mercurial > repos > galaxyp > openms_speclibsearcher
comparison SpecLibSearcher.xml @ 8:3aa3b656e624 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:12:08 +0000 |
parents | 863a35a84426 |
children | 2d6e49acbb56 |
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7:d5bc0ce9f15e | 8:3aa3b656e624 |
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1 <?xml version='1.0' encoding='UTF-8'?> | 1 <?xml version='1.0' encoding='UTF-8'?> |
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> | 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
3 <!--Proposed Tool Section: [Identification]--> | 3 <!--Proposed Tool Section: [Identification]--> |
4 <tool id="SpecLibSearcher" name="SpecLibSearcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="SpecLibSearcher" name="SpecLibSearcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.</description> | 5 <description>Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">SpecLibSearcher</token> | 7 <token name="@EXECUTABLE@">SpecLibSearcher</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@ |
16 #import re | 14 #import re |
17 | 15 |
18 ## Preprocessing | 16 ## Preprocessing |
19 mkdir in && | 17 mkdir in_cond.in && |
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } | 18 #if $in_cond.in_select == "no" |
19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && | |
20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} | |
21 #else | |
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && | |
23 #end if | |
21 mkdir lib && | 24 mkdir lib && |
22 ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' && | 25 ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' && |
23 mkdir out && | 26 mkdir out && |
27 mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && | |
24 | 28 |
25 ## Main program call | 29 ## Main program call |
26 | 30 |
27 set -o pipefail && | 31 set -o pipefail && |
28 @EXECUTABLE@ -write_ctd ./ && | 32 @EXECUTABLE@ -write_ctd ./ && |
29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | 33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | 34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
31 -in | 35 -in |
32 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | 36 #if $in_cond.in_select == "no" |
37 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} | |
38 #else | |
39 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' | |
40 #end if | |
33 -lib | 41 -lib |
34 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' | 42 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' |
35 -out | 43 -out |
36 ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("idxml")) for _ in $in if _])} | 44 ${' '.join(["'out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("idxml")) for i, f in enumerate($in_cond.in) if f])} |
37 | 45 |
38 ## Postprocessing | 46 ## Postprocessing |
39 ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("idxml")} for _ in $out if _])} | 47 ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("idxml")} for i, f in enumerate($in_cond.in) if f])} |
40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS | 48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
41 && mv '@EXECUTABLE@.ctd' '$ctd_out' | 49 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
42 #end if]]></command> | 50 #end if]]></command> |
43 <configfiles> | 51 <configfiles> |
44 <inputs name="args_json" data_style="paths"/> | 52 <inputs name="args_json" data_style="paths"/> |
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
46 </configfiles> | 54 </configfiles> |
47 <inputs> | 55 <inputs> |
48 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files" help=" select mzml data sets(s)"/> | 56 <conditional name="in_cond"> |
49 <param name="lib" argument="-lib" type="data" format="msp" optional="false" label="searchable spectral library (MSP format)" help=" select msp data sets(s)"/> | 57 <param name="in_select" type="select" label="Run tool in batch mode for -in"> |
50 <param name="compare_function" argument="-compare_function" type="select" optional="false" label="function for similarity comparison" help=""> | 58 <option value="no">No: process all datasets jointly</option> |
59 <option value="yes">Yes: process each dataset in an independent job</option> | |
60 </param> | |
61 <when value="no"> | |
62 <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files" help=" select mzml data sets(s)"/> | |
63 </when> | |
64 <when value="yes"> | |
65 <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files" help=" select mzml data sets(s)"/> | |
66 </when> | |
67 </conditional> | |
68 <param argument="-lib" type="data" format="msp" optional="false" label="searchable spectral library (MSP format)" help=" select msp data sets(s)"/> | |
69 <param argument="-compare_function" type="select" optional="true" label="function for similarity comparison" help=""> | |
51 <option value="PeakAlignment">PeakAlignment</option> | 70 <option value="PeakAlignment">PeakAlignment</option> |
52 <option value="SpectrumAlignmentScore">SpectrumAlignmentScore</option> | 71 <option value="SpectrumAlignmentScore">SpectrumAlignmentScore</option> |
53 <option value="SpectrumCheapDPCorr">SpectrumCheapDPCorr</option> | 72 <option value="SpectrumCheapDPCorr">SpectrumCheapDPCorr</option> |
54 <option value="SpectrumPrecursorComparator">SpectrumPrecursorComparator</option> | 73 <option value="SpectrumPrecursorComparator">SpectrumPrecursorComparator</option> |
55 <option value="SteinScottImproveScore">SteinScottImproveScore</option> | 74 <option value="SteinScottImproveScore">SteinScottImproveScore</option> |
56 <option value="ZhangSimilarityScore" selected="true">ZhangSimilarityScore</option> | 75 <option value="ZhangSimilarityScore" selected="true">ZhangSimilarityScore</option> |
57 <expand macro="list_string_san"/> | 76 <expand macro="list_string_san" name="compare_function"/> |
58 </param> | 77 </param> |
59 <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false"> | 78 <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false"> |
60 <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/> | 79 <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/> |
61 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help=""> | 80 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> |
62 <option value="ppm" selected="true">ppm</option> | 81 <option value="ppm" selected="true">ppm</option> |
63 <option value="Da">Da</option> | 82 <option value="Da">Da</option> |
64 <expand macro="list_string_san"/> | 83 <expand macro="list_string_san" name="mass_tolerance_unit"/> |
65 </param> | 84 </param> |
66 <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/> | 85 <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/> |
67 <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/> | 86 <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/> |
68 <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)"> | 87 <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)"> |
69 <expand macro="list_integer_valsan"/> | 88 <expand macro="list_integer_valsan" name="isotopes"/> |
70 </param> | 89 </param> |
71 </section> | 90 </section> |
72 <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false"> | 91 <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false"> |
73 <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance" help=""/> | 92 <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance" help=""/> |
74 </section> | 93 </section> |
81 <param name="max_peaks" argument="-filter:max_peaks" type="integer" optional="true" value="150" label="Use only the top <number> of peaks" help=""/> | 100 <param name="max_peaks" argument="-filter:max_peaks" type="integer" optional="true" value="150" label="Use only the top <number> of peaks" help=""/> |
82 <param name="cut_peaks_below" argument="-filter:cut_peaks_below" type="integer" optional="true" value="1000" label="Remove all peaks which are lower than 1/<number> of the highest peaks" help="Default equals all peaks which are lower than 0.001 of the maximum intensity peak"/> | 101 <param name="cut_peaks_below" argument="-filter:cut_peaks_below" type="integer" optional="true" value="1000" label="Remove all peaks which are lower than 1/<number> of the highest peaks" help="Default equals all peaks which are lower than 0.001 of the maximum intensity peak"/> |
83 </section> | 102 </section> |
84 <section name="modifications" title="Modifications Options" help="" expanded="false"> | 103 <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)'"> | 104 <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> | 105 <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> | 106 <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> | 107 <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> | 108 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> |
91 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> | 109 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> |
1450 <option value="Glu->Lys (E)">Glu->Lys (E)</option> | 1468 <option value="Glu->Lys (E)">Glu->Lys (E)</option> |
1451 <option value="Glu->Met (E)">Glu->Met (E)</option> | 1469 <option value="Glu->Met (E)">Glu->Met (E)</option> |
1452 <option value="Glu->Phe (E)">Glu->Phe (E)</option> | 1470 <option value="Glu->Phe (E)">Glu->Phe (E)</option> |
1453 <option value="Glu->Pro (E)">Glu->Pro (E)</option> | 1471 <option value="Glu->Pro (E)">Glu->Pro (E)</option> |
1454 <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> | 1472 <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> |
1455 <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> | |
1456 <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> | 1473 <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> |
1457 <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> | 1474 <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> |
1458 <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> | 1475 <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> |
1459 <option value="Glu->Ser (E)">Glu->Ser (E)</option> | 1476 <option value="Glu->Ser (E)">Glu->Ser (E)</option> |
1460 <option value="Glu->Thr (E)">Glu->Thr (E)</option> | 1477 <option value="Glu->Thr (E)">Glu->Thr (E)</option> |
3010 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> | 3027 <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> | 3028 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> |
3012 <option value="ZGB (K)">ZGB (K)</option> | 3029 <option value="ZGB (K)">ZGB (K)</option> |
3013 <option value="ZGB (N-term)">ZGB (N-term)</option> | 3030 <option value="ZGB (N-term)">ZGB (N-term)</option> |
3014 <option value="ZQG (K)">ZQG (K)</option> | 3031 <option value="ZQG (K)">ZQG (K)</option> |
3015 <expand macro="list_string_san"/> | 3032 <expand macro="list_string_san" name="fixed"/> |
3016 </param> | 3033 </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)'"> | 3034 <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> | 3035 <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> | 3036 <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> | 3037 <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> | 3038 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> |
3023 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> | 3039 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> |
4382 <option value="Glu->Lys (E)">Glu->Lys (E)</option> | 4398 <option value="Glu->Lys (E)">Glu->Lys (E)</option> |
4383 <option value="Glu->Met (E)">Glu->Met (E)</option> | 4399 <option value="Glu->Met (E)">Glu->Met (E)</option> |
4384 <option value="Glu->Phe (E)">Glu->Phe (E)</option> | 4400 <option value="Glu->Phe (E)">Glu->Phe (E)</option> |
4385 <option value="Glu->Pro (E)">Glu->Pro (E)</option> | 4401 <option value="Glu->Pro (E)">Glu->Pro (E)</option> |
4386 <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> | 4402 <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> |
4387 <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> | |
4388 <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> | 4403 <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> |
4389 <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> | 4404 <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> |
4390 <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> | 4405 <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> |
4391 <option value="Glu->Ser (E)">Glu->Ser (E)</option> | 4406 <option value="Glu->Ser (E)">Glu->Ser (E)</option> |
4392 <option value="Glu->Thr (E)">Glu->Thr (E)</option> | 4407 <option value="Glu->Thr (E)">Glu->Thr (E)</option> |
5942 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> | 5957 <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> | 5958 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> |
5944 <option value="ZGB (K)">ZGB (K)</option> | 5959 <option value="ZGB (K)">ZGB (K)</option> |
5945 <option value="ZGB (N-term)">ZGB (N-term)</option> | 5960 <option value="ZGB (N-term)">ZGB (N-term)</option> |
5946 <option value="ZQG (K)">ZQG (K)</option> | 5961 <option value="ZQG (K)">ZQG (K)</option> |
5947 <expand macro="list_string_san"/> | 5962 <expand macro="list_string_san" name="variable"/> |
5948 </param> | 5963 </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=""/> | 5964 <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> | 5965 </section> |
5951 <expand macro="adv_opts_macro"> | 5966 <expand macro="adv_opts_macro"> |
5952 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 5967 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
5953 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 5968 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
5954 <expand macro="list_string_san"/> | 5969 <expand macro="list_string_san" name="test"/> |
5955 </param> | 5970 </param> |
5956 </expand> | 5971 </expand> |
5957 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 5972 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
5958 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 5973 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
5959 </param> | 5974 </param> |
5960 </inputs> | 5975 </inputs> |
5961 <outputs> | 5976 <outputs> |
5962 <collection type="list" name="out" label="${tool.name} on ${on_string}: out"> | 5977 <collection type="list" name="out" label="${tool.name} on ${on_string}: out"> |
5963 <discover_datasets directory="out" format="idxml" pattern="__name__"/> | 5978 <discover_datasets directory="out" recurse="true" format="idxml" pattern="__name__"/> |
5964 </collection> | 5979 </collection> |
5965 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 5980 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
5966 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 5981 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
5967 </data> | 5982 </data> |
5968 </outputs> | 5983 </outputs> |
5969 <tests> | 5984 <tests><!-- TOPP_SpecLibSearcher_1 --> |
5970 <expand macro="autotest_SpecLibSearcher"/> | 5985 <test expect_num_outputs="2"> |
5971 <expand macro="manutest_SpecLibSearcher"/> | 5986 <section name="adv_opts"> |
5987 <param name="force" value="false"/> | |
5988 <param name="test" value="true"/> | |
5989 </section> | |
5990 <conditional name="in_cond"> | |
5991 <param name="in" value="SpecLibSearcher_1.mzML"/> | |
5992 </conditional> | |
5993 <param name="lib" value="SpecLibSearcher_1.MSP"/> | |
5994 <output_collection name="out" count="1"/> | |
5995 <param name="compare_function" value="ZhangSimilarityScore"/> | |
5996 <section name="precursor"> | |
5997 <param name="mass_tolerance" value="3.0"/> | |
5998 <param name="mass_tolerance_unit" value="Da"/> | |
5999 <param name="min_charge" value="1"/> | |
6000 <param name="max_charge" value="5"/> | |
6001 <param name="isotopes" value="0 1"/> | |
6002 </section> | |
6003 <section name="fragment"> | |
6004 <param name="mass_tolerance" value="10.0"/> | |
6005 </section> | |
6006 <section name="report"> | |
6007 <param name="top_hits" value="10"/> | |
6008 </section> | |
6009 <section name="filter"> | |
6010 <param name="remove_peaks_below_threshold" value="2.01"/> | |
6011 <param name="min_peaks" value="5"/> | |
6012 <param name="max_peaks" value="150"/> | |
6013 <param name="cut_peaks_below" value="1000"/> | |
6014 </section> | |
6015 <section name="modifications"> | |
6016 <param name="fixed"/> | |
6017 <param name="variable"/> | |
6018 <param name="variable_max_per_peptide" value="2"/> | |
6019 </section> | |
6020 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
6021 <output name="ctd_out" ftype="xml"> | |
6022 <assert_contents> | |
6023 <is_valid_xml/> | |
6024 </assert_contents> | |
6025 </output> | |
6026 </test> | |
5972 </tests> | 6027 </tests> |
5973 <help><![CDATA[Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library. | 6028 <help><![CDATA[Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library. |
5974 | 6029 |
5975 | 6030 |
5976 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_SpecLibSearcher.html]]></help> | 6031 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpecLibSearcher.html]]></help> |
5977 <expand macro="references"/> | 6032 <expand macro="references"/> |
5978 </tool> | 6033 </tool> |