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comparison LuciphorAdapter.xml @ 14:bf2bf60c8af2 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 19:03:21 +0000
parents cab9b21eabf9
children
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13:cab9b21eabf9 14:bf2bf60c8af2
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: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="LuciphorAdapter" name="LuciphorAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05"> 4 <tool id="LuciphorAdapter" name="LuciphorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Modification site localisation using LuciPHOr2.</description> 5 <description>Modification site localisation using LuciPHOr2.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">LuciphorAdapter</token> 7 <token name="@EXECUTABLE@">LuciphorAdapter</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@
43 <configfiles> 41 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 42 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(dirname \$(realpath \$(which luciphor2)))/luciphor2.jar", "num_threads": "\${GALAXY_SLOTS:-1}", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 43 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(dirname \$(realpath \$(which luciphor2)))/luciphor2.jar", "num_threads": "\${GALAXY_SLOTS:-1}", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 44 </configfiles>
47 <inputs> 45 <inputs>
48 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input spectrum file" help=" select mzml data sets(s)"/> 46 <param argument="-in" type="data" format="mzml" optional="false" label="Input spectrum file" help=" select mzml data sets(s)"/>
49 <param name="id" argument="-id" type="data" format="idxml" optional="false" label="Protein/peptide identifications file" help=" select idxml data sets(s)"/> 47 <param argument="-id" type="data" format="idxml" optional="false" label="Protein/peptide identifications file" help=" select idxml data sets(s)"/>
50 <param name="fragment_method" argument="-fragment_method" display="radio" type="select" optional="false" label="Fragmentation method" help=""> 48 <param argument="-fragment_method" type="select" optional="true" label="Fragmentation method" help="">
51 <option value="CID" selected="true">CID</option> 49 <option value="CID" selected="true">CID</option>
52 <option value="HCD">HCD</option> 50 <option value="HCD">HCD</option>
53 <expand macro="list_string_san"/> 51 <expand macro="list_string_san" name="fragment_method"/>
54 </param> 52 </param>
55 <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Tolerance of the peaks in the fragment spectrum" help=""/> 53 <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Tolerance of the peaks in the fragment spectrum" help=""/>
56 <param name="fragment_error_units" argument="-fragment_error_units" display="radio" type="select" optional="false" label="Unit of fragment mass tolerance" help=""> 54 <param argument="-fragment_error_units" type="select" optional="true" label="Unit of fragment mass tolerance" help="">
57 <option value="Da" selected="true">Da</option> 55 <option value="Da" selected="true">Da</option>
58 <option value="ppm">ppm</option> 56 <option value="ppm">ppm</option>
59 <expand macro="list_string_san"/> 57 <expand macro="list_string_san" name="fragment_error_units"/>
60 </param> 58 </param>
61 <param name="min_mz" argument="-min_mz" type="float" optional="true" value="150.0" label="Do not consider peaks below this value for matching fragment ions" help=""/> 59 <param argument="-min_mz" type="float" optional="true" value="150.0" label="Do not consider peaks below this value for matching fragment ions" help=""/>
62 <param name="target_modifications" argument="-target_modifications" multiple="true" type="select" optional="true" label="List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'"> 60 <param argument="-target_modifications" multiple="true" type="select" optional="true" label="List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
63 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 61 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
64 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 62 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
65 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 63 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
66 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 64 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
67 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 65 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
1426 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 1424 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
1427 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1425 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1428 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1426 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1429 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1427 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1430 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1428 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1431 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1432 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1429 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1433 <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> 1430 <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>
1434 <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> 1431 <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>
1435 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1432 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1436 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1433 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
2986 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 2983 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
2987 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 2984 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
2988 <option value="ZGB (K)">ZGB (K)</option> 2985 <option value="ZGB (K)">ZGB (K)</option>
2989 <option value="ZGB (N-term)">ZGB (N-term)</option> 2986 <option value="ZGB (N-term)">ZGB (N-term)</option>
2990 <option value="ZQG (K)">ZQG (K)</option> 2987 <option value="ZQG (K)">ZQG (K)</option>
2991 <expand macro="list_string_san"/> 2988 <expand macro="list_string_san" name="target_modifications"/>
2992 </param> 2989 </param>
2993 <param name="neutral_losses" argument="-neutral_losses" type="text" optional="true" value="&quot;sty -H3PO4 -97.97690&quot;" label="List the types of neutral losses that you want to conside" help="The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = &lt;RESDIUES&gt; -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 2990 <param argument="-neutral_losses" type="text" optional="true" value="&quot;sty -H3PO4 -97.97690&quot;" label="List the types of neutral losses that you want to conside" help="The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = &lt;RESDIUES&gt; -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
2994 <expand macro="list_string_val"/> 2991 <expand macro="list_string_val" name="neutral_losses"/>
2995 <expand macro="list_string_san"/> 2992 <expand macro="list_string_san" name="neutral_losses"/>
2996 </param> 2993 </param>
2997 <param name="decoy_mass" argument="-decoy_mass" type="float" optional="true" min="1.0" value="79.966331" label="How much to add to an amino acid to make it a decoy" help=""/> 2994 <param argument="-decoy_mass" type="float" optional="true" min="1.0" value="79.966331" label="How much to add to an amino acid to make it a decoy" help=""/>
2998 <param name="decoy_neutral_losses" argument="-decoy_neutral_losses" type="text" optional="true" value="&quot;X -H3PO4 -97.97690&quot;" label="For handling the neutral loss from a decoy sequence" help="The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 2995 <param argument="-decoy_neutral_losses" type="text" optional="true" value="&quot;X -H3PO4 -97.97690&quot;" label="For handling the neutral loss from a decoy sequence" help="The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
2999 <expand macro="list_string_val"/> 2996 <expand macro="list_string_val" name="decoy_neutral_losses"/>
3000 <expand macro="list_string_san"/> 2997 <expand macro="list_string_san" name="decoy_neutral_losses"/>
3001 </param> 2998 </param>
3002 <param name="max_charge_state" argument="-max_charge_state" type="integer" optional="true" min="1" value="5" label="Do not consider PSMs with a charge state above this value" help=""/> 2999 <param argument="-max_charge_state" type="integer" optional="true" min="1" value="5" label="Do not consider PSMs with a charge state above this value" help=""/>
3003 <param name="max_peptide_length" argument="-max_peptide_length" type="integer" optional="true" min="1" value="40" label="Restrict scoring to peptides with a length shorter than this value" help=""/> 3000 <param argument="-max_peptide_length" type="integer" optional="true" min="1" value="40" label="Restrict scoring to peptides with a length shorter than this value" help=""/>
3004 <param name="max_num_perm" argument="-max_num_perm" type="integer" optional="true" min="1" value="16384" label="Maximum number of permutations a sequence can have" help=""/> 3001 <param argument="-max_num_perm" type="integer" optional="true" min="1" value="16384" label="Maximum number of permutations a sequence can have" help=""/>
3005 <param name="modeling_score_threshold" argument="-modeling_score_threshold" type="float" optional="true" min="0.0" value="0.95" label="Minimum score a PSM needs to be considered for modeling" help=""/> 3002 <param argument="-modeling_score_threshold" type="float" optional="true" min="0.0" value="0.95" label="Minimum score a PSM needs to be considered for modeling" help=""/>
3006 <param name="scoring_threshold" argument="-scoring_threshold" type="float" optional="true" min="0.0" value="0.0" label="PSMs below this value will be discarded" help=""/> 3003 <param argument="-scoring_threshold" type="float" optional="true" min="0.0" value="0.0" label="PSMs below this value will be discarded" help=""/>
3007 <param name="min_num_psms_model" argument="-min_num_psms_model" type="integer" optional="true" min="1" value="50" label="The minimum number of PSMs you need for any charge state in order to build a model for it" help=""/> 3004 <param argument="-min_num_psms_model" type="integer" optional="true" min="1" value="50" label="The minimum number of PSMs you need for any charge state in order to build a model for it" help=""/>
3008 <param name="run_mode" argument="-run_mode" display="radio" type="select" optional="false" label="Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported" help=""> 3005 <param argument="-run_mode" type="select" optional="true" label="Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported" help="">
3009 <option value="0" selected="true">0</option> 3006 <option value="0" selected="true">0</option>
3010 <option value="1">1</option> 3007 <option value="1">1</option>
3011 <expand macro="list_string_san"/> 3008 <expand macro="list_string_san" name="run_mode"/>
3012 </param> 3009 </param>
3013 <param name="rt_tolerance" argument="-rt_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used)" help=""/> 3010 <param argument="-rt_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used)" help=""/>
3014 <expand macro="adv_opts_macro"> 3011 <expand macro="adv_opts_macro">
3015 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 3012 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
3016 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 3013 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
3017 <expand macro="list_string_san"/> 3014 <expand macro="list_string_san" name="test"/>
3018 </param> 3015 </param>
3019 </expand> 3016 </expand>
3020 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 3017 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
3021 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 3018 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
3022 </param> 3019 </param>
3025 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 3022 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
3026 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 3023 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
3027 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 3024 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
3028 </data> 3025 </data>
3029 </outputs> 3026 </outputs>
3030 <tests> 3027 <tests><!-- TOPP_LuciphorAdapter_1 -->
3031 <expand macro="autotest_LuciphorAdapter"/> 3028 <test expect_num_outputs="2">
3032 <expand macro="manutest_LuciphorAdapter"/> 3029 <section name="adv_opts">
3030 <param name="force" value="false"/>
3031 <param name="test" value="true"/>
3032 </section>
3033 <param name="in" value="LuciphorAdapter_1_input.mzML"/>
3034 <param name="id" value="LuciphorAdapter_1_input.idXML"/>
3035 <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
3036 <param name="fragment_method" value="CID"/>
3037 <param name="fragment_mass_tolerance" value="0.5"/>
3038 <param name="fragment_error_units" value="Da"/>
3039 <param name="min_mz" value="150.0"/>
3040 <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/>
3041 <param name="neutral_losses" value="&quot;sty -H3PO4 -97.97690&quot;"/>
3042 <param name="decoy_mass" value="79.966331"/>
3043 <param name="decoy_neutral_losses" value="&quot;X -H3PO4 -97.97690&quot;"/>
3044 <param name="max_charge_state" value="5"/>
3045 <param name="max_peptide_length" value="40"/>
3046 <param name="max_num_perm" value="16384"/>
3047 <param name="modeling_score_threshold" value="0.95"/>
3048 <param name="scoring_threshold" value="0.0"/>
3049 <param name="min_num_psms_model" value="1"/>
3050 <param name="run_mode" value="0"/>
3051 <param name="rt_tolerance" value="0.01"/>
3052 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3053 <output name="ctd_out" ftype="xml">
3054 <assert_contents>
3055 <is_valid_xml/>
3056 </assert_contents>
3057 </output>
3058 </test>
3033 </tests> 3059 </tests>
3034 <help><![CDATA[Modification site localisation using LuciPHOr2. 3060 <help><![CDATA[Modification site localisation using LuciPHOr2.
3035 3061
3036 3062
3037 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_LuciphorAdapter.html]]></help> 3063 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_LuciphorAdapter.html]]></help>
3038 <expand macro="references"/> 3064 <expand macro="references"/>
3039 </tool> 3065 </tool>