Mercurial > repos > galaxyp > openms_pepnovoadapter

comparison PepNovoAdapter.xml @ 4:533859c7e75f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:18:33 +0000
parents 3bfc9aba4809
children
comparison
equal deleted inserted replaced
3:e570599ec9f2 4:533859c7e75f
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="PepNovoAdapter" name="PepNovoAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="PepNovoAdapter" name="PepNovoAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format.</description> 5 <description>Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PepNovoAdapter</token> 7 <token name="@EXECUTABLE@">PepNovoAdapter</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@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"pepnovo_executable": "pepnovo", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"pepnovo_executable": "pepnovo", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <inputs>
44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> 42 <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
45 <param name="model_directory" argument="-model_directory" type="select" optional="false" label="Name of the directory where the model files are kept" help=""> 43 <param name="model_directory" argument="-model_directory" type="select" optional="false" label="Name of the directory where the model files are kept" help="">
46 <options from_data_table="pepnovo_models"> 44 <options from_data_table="pepnovo_models">
47 <column name="name" index="0"/> 45 <column name="name" index="0"/>
48 <column name="value" index="2"/> 46 <column name="value" index="2"/>
49 <filter type="unique_value" name="unique_set" column="0"/> 47 <filter type="unique_value" name="unique_set" column="0"/>
50 <validator type="no_options" message="No model directory available"/> 48 <validator type="no_options" message="No model directory available"/>
51 </options> 49 </options>
52 </param> 50 </param>
53 <param name="correct_pm" argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/> 51 <param argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/>
54 <param name="use_spectrum_charge" argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/> 52 <param argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/>
55 <param name="use_spectrum_mz" argument="-use_spectrum_mz" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct the precursor m/z value that appears in the file" help=""/> 53 <param argument="-use_spectrum_mz" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct the precursor m/z value that appears in the file" help=""/>
56 <param name="no_quality_filter" argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/> 54 <param argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/>
57 <param name="fragment_tolerance" argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/> 55 <param argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/>
58 <param name="pm_tolerance" argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/> 56 <param argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/>
59 <param name="model" argument="-model" type="select" label="Name of the model that should be used" help=""> 57 <param name="model" argument="-model" type="select" label="Name of the model that should be used" help="">
60 <options from_data_table="pepnovo_models"> 58 <options from_data_table="pepnovo_models">
61 <column name="name" index="1"/> 59 <column name="name" index="1"/>
62 <column name="value" index="1"/> 60 <column name="value" index="1"/>
63 <filter type="param_value" ref="model_directory" column="2"/> 61 <filter type="param_value" ref="model_directory" column="2"/>
64 <filter type="unique_value" column="1"/> 62 <filter type="unique_value" column="1"/>
65 <validator type="no_options" message="No model available"/> 63 <validator type="no_options" message="No model available"/>
66 </options> 64 </options>
67 </param> 65 </param>
68 <param name="digest" argument="-digest" display="radio" type="select" optional="false" label="Enzyme used for digestion (default TRYPSIN)" help=""> 66 <param argument="-digest" type="select" optional="true" label="Enzyme used for digestion (default TRYPSIN)" help="">
69 <option value="TRYPSIN" selected="true">TRYPSIN</option> 67 <option value="TRYPSIN" selected="true">TRYPSIN</option>
70 <option value="NON_SPECIFIC">NON_SPECIFIC</option> 68 <option value="NON_SPECIFIC">NON_SPECIFIC</option>
71 <expand macro="list_string_san"/> 69 <expand macro="list_string_san" name="digest"/>
72 </param> 70 </param>
73 <param name="tag_length" argument="-tag_length" type="integer" optional="true" value="-1" label="Returns peptide sequence of the specified length (only lengths 3-6 are allowed)" help=""/> 71 <param argument="-tag_length" type="integer" optional="true" value="-1" label="Returns peptide sequence of the specified length (only lengths 3-6 are allowed)" help=""/>
74 <param name="num_solutions" argument="-num_solutions" type="integer" optional="true" min="1" max="2000" value="20" label="Number of solutions to be computed" help=""/> 72 <param argument="-num_solutions" type="integer" optional="true" min="1" max="2000" value="20" label="Number of solutions to be computed" help=""/>
75 <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)'"> 73 <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)'">
76 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 74 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
77 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 75 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
78 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 76 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
79 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 77 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
80 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 78 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
1439 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 1437 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
1440 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1438 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1441 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1439 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1442 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1440 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1443 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1441 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1444 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1445 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1442 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1446 <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> 1443 <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>
1447 <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> 1444 <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>
1448 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1445 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1449 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1446 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
2999 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 2996 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
3000 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 2997 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
3001 <option value="ZGB (K)">ZGB (K)</option> 2998 <option value="ZGB (K)">ZGB (K)</option>
3002 <option value="ZGB (N-term)">ZGB (N-term)</option> 2999 <option value="ZGB (N-term)">ZGB (N-term)</option>
3003 <option value="ZQG (K)">ZQG (K)</option> 3000 <option value="ZQG (K)">ZQG (K)</option>
3004 <expand macro="list_string_san"/> 3001 <expand macro="list_string_san" name="fixed_modifications"/>
3005 </param> 3002 </param>
3006 <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)'"> 3003 <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)'">
3007 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 3004 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
3008 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 3005 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
3009 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 3006 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
3010 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 3007 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
3011 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 3008 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
4370 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 4367 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
4371 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4368 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4372 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4369 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4373 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4370 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
4374 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 4371 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
4375 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4376 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 4372 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4377 <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> 4373 <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>
4378 <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> 4374 <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>
4379 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 4375 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4380 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4376 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
5930 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 5926 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
5931 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 5927 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
5932 <option value="ZGB (K)">ZGB (K)</option> 5928 <option value="ZGB (K)">ZGB (K)</option>
5933 <option value="ZGB (N-term)">ZGB (N-term)</option> 5929 <option value="ZGB (N-term)">ZGB (N-term)</option>
5934 <option value="ZQG (K)">ZQG (K)</option> 5930 <option value="ZQG (K)">ZQG (K)</option>
5935 <expand macro="list_string_san"/> 5931 <expand macro="list_string_san" name="variable_modifications"/>
5936 </param> 5932 </param>
5937 <expand macro="adv_opts_macro"> 5933 <expand macro="adv_opts_macro">
5938 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 5934 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
5939 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 5935 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
5940 <expand macro="list_string_san"/> 5936 <expand macro="list_string_san" name="test"/>
5941 </param> 5937 </param>
5942 </expand> 5938 </expand>
5943 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 5939 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
5944 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 5940 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
5945 </param> 5941 </param>
5948 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 5944 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
5949 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 5945 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
5950 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 5946 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
5951 </data> 5947 </data>
5952 </outputs> 5948 </outputs>
5953 <tests> 5949 <tests><test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection
5954 <expand macro="autotest_PepNovoAdapter"/> 5950 unclear https://github.com/OpenMS/OpenMS/issues/4719)-->
5955 <expand macro="manutest_PepNovoAdapter"/> 5951 <param name="adv_opts|test" value="true"/>
5956 </tests> 5952 <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
5953 <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
5954 <param name="model" value="LTQ_COMP"/>
5955 </test>
5956 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
5957 <param name="adv_opts|test" value="true"/>
5958 <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
5959 <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
5960 <param name="model" value="LTQ_COMP"/>
5961 </test>
5962 </tests>
5957 <help><![CDATA[Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format. 5963 <help><![CDATA[Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format.
5958 5964
5959 5965
5960 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PepNovoAdapter.html]]></help> 5966 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PepNovoAdapter.html]]></help>
5961 <expand macro="references"/> 5967 <expand macro="references"/>
5962 </tool> 5968 </tool>