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comparison OMSSAAdapter.xml @ 4:1672e6be33d3 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 19:10:09 +0000
parents 886991df53f7
children
comparison
equal deleted inserted replaced
3:b2b286ee9131 4:1672e6be33d3
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="OMSSAAdapter" name="OMSSAAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="OMSSAAdapter" name="OMSSAAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Annotates MS/MS spectra using OMSSA.</description> 5 <description>Annotates MS/MS spectra using OMSSA.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OMSSAAdapter</token> 7 <token name="@EXECUTABLE@">OMSSAAdapter</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@
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir out && 19 mkdir out &&
22 mkdir database && 20 mkdir database &&
23 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && 21 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
24 22
25 makeblastdb -dbtype prot -in 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && 23 makeblastdb -dbtype prot -blastdb_version 4 -in 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
26 ## Main program call 24 ## Main program call
27 25
28 set -o pipefail && 26 set -o pipefail &&
29 @EXECUTABLE@ -write_ctd ./ && 27 @EXECUTABLE@ -write_ctd ./ &&
30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 28 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
44 <configfiles> 42 <configfiles>
45 <inputs name="args_json" data_style="paths"/> 43 <inputs name="args_json" data_style="paths"/>
46 <configfile name="hardcoded_json"><![CDATA[{"omssa_executable": "\$(dirname \$(realpath \$(which omssacl)))/omssacl", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 44 <configfile name="hardcoded_json"><![CDATA[{"omssa_executable": "\$(dirname \$(realpath \$(which omssacl)))/omssacl", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
47 </configfiles> 45 </configfiles>
48 <inputs> 46 <inputs>
49 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/> 47 <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
50 <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance" help=""/> 48 <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance" help=""/>
51 <param name="precursor_error_units" argument="-precursor_error_units" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help=""> 49 <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
52 <option value="Da">Da</option> 50 <option value="Da">Da</option>
53 <option value="ppm" selected="true">ppm</option> 51 <option value="ppm" selected="true">ppm</option>
54 <expand macro="list_string_san"/> 52 <expand macro="list_string_san" name="precursor_error_units"/>
55 </param> 53 </param>
56 <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.3" label="Fragment mass error in Dalton" help=""/> 54 <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.3" label="Fragment mass error in Dalton" help=""/>
57 <param name="database" argument="-database" type="data" format="fasta" optional="false" label="NCBI formatted FASTA files" help="The .psq filename should be given, e.g. 'SwissProt.fasta.psq'. If the filename does not end in '.psq' (e.g., SwissProt.fasta) the psq suffix will be added automatically. Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' select fasta data sets(s)"/> 55 <param argument="-database" type="data" format="fasta" optional="false" label="NCBI formatted FASTA files" help="The .psq filename should be given, e.g. 'SwissProt.fasta.psq'. If the filename does not end in '.psq' (e.g., SwissProt.fasta) the psq suffix will be added automatically. Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
58 <param name="min_precursor_charge" argument="-min_precursor_charge" type="integer" optional="true" value="1" label="Minimum precursor ion charge" help=""/> 56 <param argument="-min_precursor_charge" type="integer" optional="true" value="1" label="Minimum precursor ion charge" help=""/>
59 <param name="max_precursor_charge" argument="-max_precursor_charge" type="integer" optional="true" value="3" label="Maximum precursor ion charge" help=""/> 57 <param argument="-max_precursor_charge" type="integer" optional="true" value="3" label="Maximum precursor ion charge" help=""/>
60 <param name="fixed_modifications" argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> 58 <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
61 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 59 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
62 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 60 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
63 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 61 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
64 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 62 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
65 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 63 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
1424 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 1422 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
1425 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1423 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1426 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1424 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1427 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1425 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1428 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1426 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1429 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1430 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1427 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1431 <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> 1428 <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>
1432 <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> 1429 <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>
1433 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1430 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1434 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1431 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
2984 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 2981 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
2985 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 2982 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
2986 <option value="ZGB (K)">ZGB (K)</option> 2983 <option value="ZGB (K)">ZGB (K)</option>
2987 <option value="ZGB (N-term)">ZGB (N-term)</option> 2984 <option value="ZGB (N-term)">ZGB (N-term)</option>
2988 <option value="ZQG (K)">ZQG (K)</option> 2985 <option value="ZQG (K)">ZQG (K)</option>
2989 <expand macro="list_string_san"/> 2986 <expand macro="list_string_san" name="fixed_modifications"/>
2990 </param> 2987 </param>
2991 <param name="variable_modifications" argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> 2988 <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
2992 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 2989 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
2993 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 2990 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
2994 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 2991 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
2995 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 2992 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
2996 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 2993 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
4355 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 4352 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
4356 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4353 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4357 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4354 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4358 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4355 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
4359 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 4356 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
4360 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4361 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 4357 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4362 <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> 4358 <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>
4363 <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> 4359 <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>
4364 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 4360 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4365 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4361 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
5915 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 5911 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
5916 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 5912 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
5917 <option value="ZGB (K)">ZGB (K)</option> 5913 <option value="ZGB (K)">ZGB (K)</option>
5918 <option value="ZGB (N-term)">ZGB (N-term)</option> 5914 <option value="ZGB (N-term)">ZGB (N-term)</option>
5919 <option value="ZQG (K)">ZQG (K)</option> 5915 <option value="ZQG (K)">ZQG (K)</option>
5920 <expand macro="list_string_san"/> 5916 <expand macro="list_string_san" name="variable_modifications"/>
5921 </param> 5917 </param>
5922 <param name="v" argument="-v" type="integer" optional="true" value="1" label="number of missed cleavages allowed" help=""/> 5918 <param argument="-v" type="integer" optional="true" value="1" label="number of missed cleavages allowed" help=""/>
5923 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> 5919 <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
5924 <option value="Trypsin" selected="true">Trypsin</option> 5920 <option value="Trypsin" selected="true">Trypsin</option>
5921 <option value="Formic_acid">Formic_acid</option>
5922 <option value="Lys-C">Lys-C</option>
5923 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
5924 <option value="Asp-N_ambic">Asp-N_ambic</option>
5925 <option value="Chymotrypsin">Chymotrypsin</option>
5925 <option value="Lys-C/P">Lys-C/P</option> 5926 <option value="Lys-C/P">Lys-C/P</option>
5927 <option value="Asp-N">Asp-N</option>
5928 <option value="CNBr">CNBr</option>
5926 <option value="PepsinA">PepsinA</option> 5929 <option value="PepsinA">PepsinA</option>
5927 <option value="TrypChymo">TrypChymo</option> 5930 <option value="TrypChymo">TrypChymo</option>
5928 <option value="Trypsin/P">Trypsin/P</option> 5931 <option value="Trypsin/P">Trypsin/P</option>
5929 <option value="CNBr">CNBr</option>
5930 <option value="Formic_acid">Formic_acid</option>
5931 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
5932 <option value="Chymotrypsin">Chymotrypsin</option>
5933 <option value="Asp-N_ambic">Asp-N_ambic</option>
5934 <option value="Lys-C">Lys-C</option>
5935 <option value="Arg-C">Arg-C</option> 5932 <option value="Arg-C">Arg-C</option>
5936 <option value="no cleavage">no cleavage</option> 5933 <option value="no cleavage">no cleavage</option>
5937 <option value="unspecific cleavage">unspecific cleavage</option> 5934 <option value="unspecific cleavage">unspecific cleavage</option>
5938 <option value="Asp-N">Asp-N</option> 5935 <expand macro="list_string_san" name="enzyme"/>
5939 <expand macro="list_string_san"/>
5940 </param> 5936 </param>
5941 <param name="hl" argument="-hl" type="integer" optional="true" value="30" label="maximum number of hits retained for one spectrum" help="Note: even when set to 1 OMSSA may report multiple hits with different charge states"/> 5937 <param argument="-hl" type="integer" optional="true" value="30" label="maximum number of hits retained for one spectrum" help="Note: even when set to 1 OMSSA may report multiple hits with different charge states"/>
5942 <param name="he" argument="-he" type="float" optional="true" value="1000.0" label="the maximum e-value allowed in the hit list" help="If you set this parameter too small (e.g., he=1), this will effectively introduce FDR filtering. Thus, allowing a less stringent FDR during post-processing will nevertheless return the (better) FDR introduced here, since mediocre hits are not even reported"/> 5938 <param argument="-he" type="float" optional="true" value="1000.0" label="the maximum e-value allowed in the hit list" help="If you set this parameter too small (e.g., he=1), this will effectively introduce FDR filtering. Thus, allowing a less stringent FDR during post-processing will nevertheless return the (better) FDR introduced here, since mediocre hits are not even reported"/>
5943 <expand macro="adv_opts_macro"> 5939 <expand macro="adv_opts_macro">
5944 <param name="pc" argument="-pc" type="integer" optional="true" value="1" label="The number of pseudocounts to add to each precursor mass bin" help=""/> 5940 <param argument="-pc" type="integer" optional="true" value="1" label="The number of pseudocounts to add to each precursor mass bin" help=""/>
5945 <param name="hs" argument="-hs" type="integer" optional="true" value="4" label="the minimum number of m/z values a spectrum must have to be searched" help=""/> 5941 <param argument="-hs" type="integer" optional="true" value="4" label="the minimum number of m/z values a spectrum must have to be searched" help=""/>
5946 <param name="tez" argument="-tez" type="integer" optional="true" value="1" label="scaling of precursor mass tolerance with charge (0 = none, 1= linear)" help=""/> 5942 <param argument="-tez" type="integer" optional="true" value="1" label="scaling of precursor mass tolerance with charge (0 = none, 1= linear)" help=""/>
5947 <param name="tom" argument="-tom" type="integer" optional="true" value="0" label="product ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact" help=""/> 5943 <param argument="-tom" type="integer" optional="true" value="0" label="product ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact" help=""/>
5948 <param name="tem" argument="-tem" type="integer" optional="true" value="0" label="precursor ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact" help=""/> 5944 <param argument="-tem" type="integer" optional="true" value="0" label="precursor ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact" help=""/>
5949 <param name="tex" argument="-tex" type="float" optional="true" value="1446.94" label="threshold in Da above which the mass of a neutron should be added in an exact mass search" help=""/> 5945 <param argument="-tex" type="float" optional="true" value="1446.94" label="threshold in Da above which the mass of a neutron should be added in an exact mass search" help=""/>
5950 <param name="zt" argument="-zt" type="integer" optional="true" value="3" label="minimum precursor charge to start considering multiply charged products" help=""/> 5946 <param argument="-zt" type="integer" optional="true" value="3" label="minimum precursor charge to start considering multiply charged products" help=""/>
5951 <param name="z1" argument="-z1" type="float" optional="true" value="0.95" label="the fraction of peaks below the precursor used to determine if the spectrum is charge +1" help=""/> 5947 <param argument="-z1" type="float" optional="true" value="0.95" label="the fraction of peaks below the precursor used to determine if the spectrum is charge +1" help=""/>
5952 <param name="zc" argument="-zc" type="integer" optional="true" value="1" label="should charge +1 be determined algorithmically (1=yes)" help=""/> 5948 <param argument="-zc" type="integer" optional="true" value="1" label="should charge +1 be determined algorithmically (1=yes)" help=""/>
5953 <param name="zcc" argument="-zcc" type="integer" optional="true" value="2" label="how should precursor charges be determined" help="(1=believe the input file,2=use the specified range)"/> 5949 <param argument="-zcc" type="integer" optional="true" value="2" label="how should precursor charges be determined" help="(1=believe the input file,2=use the specified range)"/>
5954 <param name="zoh" argument="-zoh" type="integer" optional="true" value="2" label="set the maximum product charge to search" help=""/> 5950 <param argument="-zoh" type="integer" optional="true" value="2" label="set the maximum product charge to search" help=""/>
5955 <param name="no" argument="-no" type="integer" optional="true" value="4" label="minimum size of peptides for no-enzyme and semi-tryptic searches" help=""/> 5951 <param argument="-no" type="integer" optional="true" value="4" label="minimum size of peptides for no-enzyme and semi-tryptic searches" help=""/>
5956 <param name="nox" argument="-nox" type="integer" optional="true" value="40" label="maximum size of peptides for no-enzyme and semi-tryptic searches" help=""/> 5952 <param argument="-nox" type="integer" optional="true" value="40" label="maximum size of peptides for no-enzyme and semi-tryptic searches" help=""/>
5957 <param name="i" argument="-i" type="text" optional="true" value="1,4" label="comma delimited list of id numbers of ions to search" help=""> 5953 <param argument="-i" type="text" optional="true" value="1,4" label="comma delimited list of id numbers of ions to search" help="">
5958 <expand macro="list_string_san"/> 5954 <expand macro="list_string_san" name="i"/>
5959 </param> 5955 </param>
5960 <param name="sp" argument="-sp" type="integer" optional="true" value="100" label="number of product ions to search" help=""/> 5956 <param argument="-sp" type="integer" optional="true" value="100" label="number of product ions to search" help=""/>
5961 <param name="sb1" argument="-sb1" type="integer" optional="true" value="1" label="should first forward" help="(e.g. b1) product ions be searched (1 = no, 0 = yes)"/> 5957 <param argument="-sb1" type="integer" optional="true" value="1" label="should first forward" help="(e.g. b1) product ions be searched (1 = no, 0 = yes)"/>
5962 <param name="sct" argument="-sct" type="integer" optional="true" value="0" label="should c terminus ions" help="(e.g. y1) be searched (1 = no, 0 = yes)"/> 5958 <param argument="-sct" type="integer" optional="true" value="0" label="should c terminus ions" help="(e.g. y1) be searched (1 = no, 0 = yes)"/>
5963 <param name="x" argument="-x" type="text" optional="true" value="0" label="comma delimited list of NCBI taxonomy ids to search (0 = all" help="This is the default)"> 5959 <param argument="-x" type="text" optional="true" value="0" label="comma delimited list of NCBI taxonomy ids to search (0 = all" help="This is the default)">
5964 <expand macro="list_string_san"/> 5960 <expand macro="list_string_san" name="x"/>
5965 </param> 5961 </param>
5966 <param name="hm" argument="-hm" type="integer" optional="true" value="2" label="the minimum number of m/z matches a sequence library peptide must have for the hit to the peptide to be recorded" help=""/> 5962 <param argument="-hm" type="integer" optional="true" value="2" label="the minimum number of m/z matches a sequence library peptide must have for the hit to the peptide to be recorded" help=""/>
5967 <param name="ht" argument="-ht" type="integer" optional="true" value="6" label="number of m/z values corresponding to the most intense peaks that must include one match to the theoretical peptide" help=""/> 5963 <param argument="-ht" type="integer" optional="true" value="6" label="number of m/z values corresponding to the most intense peaks that must include one match to the theoretical peptide" help=""/>
5968 <param name="mm" argument="-mm" type="integer" optional="true" value="128" label="the maximum number of mass ladders to generate per database peptide" help=""/> 5964 <param argument="-mm" type="integer" optional="true" value="128" label="the maximum number of mass ladders to generate per database peptide" help=""/>
5969 <param name="mnm" argument="-mnm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="n-term methionine should not be cleaved" help=""/> 5965 <param argument="-mnm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="n-term methionine should not be cleaved" help=""/>
5970 <param name="is" argument="-is" type="float" optional="true" value="0.0" label="evalue threshold to include a sequence in the iterative search, 0 = all" help=""/> 5966 <param argument="-is" type="float" optional="true" value="0.0" label="evalue threshold to include a sequence in the iterative search, 0 = all" help=""/>
5971 <param name="ir" argument="-ir" type="float" optional="true" value="0.0" label="evalue threshold to replace a hit, 0 = only if bette" help=""/> 5967 <param argument="-ir" type="float" optional="true" value="0.0" label="evalue threshold to replace a hit, 0 = only if bette" help=""/>
5972 <param name="ii" argument="-ii" type="float" optional="true" value="0.0" label="evalue threshold to iteratively search a spectrum again, 0 = always" help=""/> 5968 <param argument="-ii" type="float" optional="true" value="0.0" label="evalue threshold to iteratively search a spectrum again, 0 = always" help=""/>
5973 <param name="chunk_size" argument="-chunk_size" type="integer" optional="true" value="0" label="Number of spectra to submit in one chunk to OMSSA" help="Chunks with more than 30k spectra will likely cause memory allocation issues with 32bit OMSSA versions (which is usually the case on Windows). To disable chunking (i.e. submit all spectra in one big chunk), set it to '0'"/> 5969 <param argument="-chunk_size" type="integer" optional="true" value="0" label="Number of spectra to submit in one chunk to OMSSA" help="Chunks with more than 30k spectra will likely cause memory allocation issues with 32bit OMSSA versions (which is usually the case on Windows). To disable chunking (i.e. submit all spectra in one big chunk), set it to '0'"/>
5974 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 5970 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
5975 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 5971 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
5976 <expand macro="list_string_san"/> 5972 <expand macro="list_string_san" name="test"/>
5977 </param> 5973 </param>
5978 </expand> 5974 </expand>
5979 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 5975 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
5980 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 5976 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
5981 </param> 5977 </param>
5984 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 5980 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
5985 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 5981 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
5986 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 5982 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
5987 </data> 5983 </data>
5988 </outputs> 5984 </outputs>
5989 <tests> 5985 <tests><!-- TOPP_OMSSAAdapter_1 -->
5990 <expand macro="autotest_OMSSAAdapter"/> 5986 <test expect_num_outputs="2">
5991 <expand macro="manutest_OMSSAAdapter"/> 5987 <section name="adv_opts">
5988 <param name="pc" value="1"/>
5989 <param name="hs" value="4"/>
5990 <param name="tez" value="1"/>
5991 <param name="tom" value="0"/>
5992 <param name="tem" value="0"/>
5993 <param name="tex" value="1446.94"/>
5994 <param name="zt" value="3"/>
5995 <param name="z1" value="0.95"/>
5996 <param name="zc" value="1"/>
5997 <param name="zcc" value="2"/>
5998 <param name="zoh" value="2"/>
5999 <param name="no" value="4"/>
6000 <param name="nox" value="40"/>
6001 <param name="i" value="1,4"/>
6002 <param name="sp" value="100"/>
6003 <param name="sb1" value="1"/>
6004 <param name="sct" value="0"/>
6005 <param name="x" value="0"/>
6006 <param name="hm" value="2"/>
6007 <param name="ht" value="6"/>
6008 <param name="mm" value="128"/>
6009 <param name="mnm" value="false"/>
6010 <param name="is" value="0.0"/>
6011 <param name="ir" value="0.0"/>
6012 <param name="ii" value="0.0"/>
6013 <param name="chunk_size" value="0"/>
6014 <param name="force" value="false"/>
6015 <param name="test" value="true"/>
6016 </section>
6017 <param name="in" value="spectra.mzML"/>
6018 <output name="out" file="OMSSAAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6019 <param name="precursor_mass_tolerance" value="5.0"/>
6020 <param name="precursor_error_units" value="ppm"/>
6021 <param name="fragment_mass_tolerance" value="0.3"/>
6022 <param name="database" value="proteins.fasta"/>
6023 <param name="min_precursor_charge" value="1"/>
6024 <param name="max_precursor_charge" value="3"/>
6025 <param name="fixed_modifications"/>
6026 <param name="variable_modifications" value="Oxidation (M)"/>
6027 <param name="v" value="1"/>
6028 <param name="enzyme" value="Trypsin"/>
6029 <param name="hl" value="30"/>
6030 <param name="he" value="1.0"/>
6031 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6032 <output name="ctd_out" ftype="xml">
6033 <assert_contents>
6034 <is_valid_xml/>
6035 </assert_contents>
6036 </output>
6037 </test>
5992 </tests> 6038 </tests>
5993 <help><![CDATA[Annotates MS/MS spectra using OMSSA. 6039 <help><![CDATA[Annotates MS/MS spectra using OMSSA.
5994 6040
5995 6041
5996 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OMSSAAdapter.html]]></help> 6042 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OMSSAAdapter.html]]></help>
5997 <expand macro="references"/> 6043 <expand macro="references"/>
5998 </tool> 6044 </tool>