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comparison SpecLibSearcher.xml @ 8:3aa3b656e624 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 19:12:08 +0000
parents 863a35a84426
children
comparison
equal deleted inserted replaced
7:d5bc0ce9f15e 8:3aa3b656e624
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 &lt;number&gt; of peaks" help=""/> 100 <param name="max_peaks" argument="-filter:max_peaks" type="integer" optional="true" value="150" label="Use only the top &lt;number&gt; 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/&lt;number&gt; 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/&lt;number&gt; 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-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 1468 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
1451 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1469 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1452 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1470 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1453 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1471 <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> 1472 <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> 1473 <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> 1474 <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> 1475 <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> 1476 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1460 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1477 <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> 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-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 4398 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
4383 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4399 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4384 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4400 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4385 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4401 <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> 4402 <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> 4403 <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> 4404 <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> 4405 <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> 4406 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4392 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4407 <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> 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>