Mercurial > repos > galaxyp > openms_epifany
comparison Epifany.xml @ 0:03e13b23a78b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
---|---|
date | Wed, 09 Sep 2020 12:47:40 +0000 |
parents | |
children | 16cdef222ea2 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:03e13b23a78b |
---|---|
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.--> | |
3 <!--Proposed Tool Section: [Utilities]--> | |
4 <tool id="Epifany" name="Epifany" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | |
5 <description>Runs a Bayesian protein inference.</description> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">Epifany</token> | |
8 <import>macros.xml</import> | |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
11 </macros> | |
12 <expand macro="requirements"/> | |
13 <expand macro="stdio"/> | |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | |
15 @EXT_FOO@ | |
16 #import re | |
17 | |
18 ## Preprocessing | |
19 mkdir in && | |
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } | |
21 mkdir out && | |
22 | |
23 ## Main program call | |
24 | |
25 set -o pipefail && | |
26 @EXECUTABLE@ -write_ctd ./ && | |
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
29 -in | |
30 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | |
31 -out | |
32 'out/output.${gxy2omsext("idxml")}' | |
33 | |
34 ## Postprocessing | |
35 && mv 'out/output.${gxy2omsext("idxml")}' '$out' | |
36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS | |
37 && mv '@EXECUTABLE@.ctd' '$ctd_out' | |
38 #end if]]></command> | |
39 <configfiles> | |
40 <inputs name="args_json" data_style="paths"/> | |
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | |
42 </configfiles> | |
43 <inputs> | |
44 <param name="in" argument="-in" type="data" format="idxml" multiple="true" optional="false" label="Input: identification results" help=" select idxml data sets(s)"/> | |
45 <param name="protein_fdr" argument="-protein_fdr" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Additionally calculate the target-decoy FDR on protein-level based on the posteriors" help=""/> | |
46 <param name="greedy_group_resolution" argument="-greedy_group_resolution" display="radio" type="select" optional="false" label="Post-process inference output with greedy resolution of shared peptides based on the parent protein probabilities" help="Also adds the resolved ambiguity groups to output"> | |
47 <option value="none" selected="true">none</option> | |
48 <option value="remove_associations_only">remove_associations_only</option> | |
49 <option value="remove_proteins_wo_evidence">remove_proteins_wo_evidence</option> | |
50 <expand macro="list_string_san"/> | |
51 </param> | |
52 <param name="max_psms_extreme_probability" argument="-max_psms_extreme_probability" type="float" optional="true" value="1.0" label="Set PSMs with probability higher than this to this maximum probability" help=""/> | |
53 <section name="algorithm" title="Parameters for the Algorithm section" help="" expanded="false"> | |
54 <param name="psm_probability_cutoff" argument="-algorithm:psm_probability_cutoff" type="float" optional="true" min="0.0" max="1.0" value="0.001" label="Remove PSMs with probabilities less than or equal this cutoff" help=""/> | |
55 <param name="top_PSMs" argument="-algorithm:top_PSMs" type="integer" optional="true" min="0" value="1" label="Consider only top X PSMs per spectrum" help="0 considers all"/> | |
56 <param name="update_PSM_probabilities" argument="-algorithm:update_PSM_probabilities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(Experimental:) Update PSM probabilities with their posteriors under consideration of the protein probabilities" help=""/> | |
57 <param name="user_defined_priors" argument="-algorithm:user_defined_priors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(Experimental:) Uses the current protein scores as user-defined priors" help=""/> | |
58 <param name="annotate_group_probabilities" argument="-algorithm:annotate_group_probabilities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Annotates group probabilities for indistinguishable protein groups (indistinguishable by experimentally observed PSMs)" help=""/> | |
59 <param name="use_ids_outside_features" argument="-algorithm:use_ids_outside_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(Only consensusXML) Also use IDs without associated features for inference?" help=""/> | |
60 <section name="model_parameters" title="Model parameters for the Bayesian network" help="" expanded="false"> | |
61 <param name="prot_prior" argument="-algorithm:model_parameters:prot_prior" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Protein prior probability ('gamma' parameter)" help="Negative values enable grid search for this param"/> | |
62 <param name="pep_emission" argument="-algorithm:model_parameters:pep_emission" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Peptide emission probability ('alpha' parameter)" help="Negative values enable grid search for this param"/> | |
63 <param name="pep_spurious_emission" argument="-algorithm:model_parameters:pep_spurious_emission" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Spurious peptide identification probability ('beta' parameter)" help="Usually much smaller than emission from proteins. Negative values enable grid search for this param"/> | |
64 <param name="pep_prior" argument="-algorithm:model_parameters:pep_prior" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Peptide prior probability (experimental, should be covered by combinations of the other params)" help=""/> | |
65 <param name="regularize" argument="-algorithm:model_parameters:regularize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Regularize the number of proteins that produce a peptide together (experimental, should be activated when using higher p-norms)" help=""/> | |
66 <param name="extended_model" argument="-algorithm:model_parameters:extended_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses information from different peptidoforms also across runs (automatically activated if an experimental design is given!)" help=""/> | |
67 </section> | |
68 <section name="loopy_belief_propagation" title="Settings for the loopy belief propagation algorithm" help="" expanded="false"> | |
69 <param name="scheduling_type" argument="-algorithm:loopy_belief_propagation:scheduling_type" display="radio" type="select" optional="false" label="(Not used yet) How to pick the next message: priority = based on difference to last message (higher = more important)" help="fifo = first in first out. random_spanning_tree = message passing follows a random spanning tree in each iteration"> | |
70 <option value="priority" selected="true">priority</option> | |
71 <option value="fifo">fifo</option> | |
72 <option value="random_spanning_tree">random_spanning_tree</option> | |
73 <expand macro="list_string_san"/> | |
74 </param> | |
75 <param name="convergence_threshold" argument="-algorithm:loopy_belief_propagation:convergence_threshold" type="float" optional="true" min="1e-09" max="1.0" value="1e-05" label="Initial threshold under which MSE difference a message is considered to be converged" help=""/> | |
76 <param name="dampening_lambda" argument="-algorithm:loopy_belief_propagation:dampening_lambda" type="float" optional="true" min="0.0" max="0.49999" value="0.001" label="Initial value for how strongly should messages be updated in each step" help="0 = new message overwrites old completely (no dampening; only recommended for trees),0.5 = equal contribution of old and new message (stay below that),In-between it will be a convex combination of both. Prevents oscillations but hinders convergence"/> | |
77 <param name="max_nr_iterations" argument="-algorithm:loopy_belief_propagation:max_nr_iterations" type="integer" optional="true" value="2147483647" label="(Unused, autodetermined) If not all messages converge, how many iterations should be done at max?" help=""/> | |
78 <param name="p_norm_inference" argument="-algorithm:loopy_belief_propagation:p_norm_inference" type="float" optional="true" value="1.0" label="P-norm used for marginalization of multidimensional factors" help="1 == sum-product inference (all configurations vote equally) (default),<= 0 == infinity = max-product inference (only best configurations propagate)The higher the value the more important high probability configurations get"/> | |
79 </section> | |
80 <section name="param_optimize" title="Settings for the parameter optimization" help="" expanded="false"> | |
81 <param name="aucweight" argument="-algorithm:param_optimize:aucweight" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="How important is AUC vs calibration of the posteriors" help="0 = maximize calibration only, 1 = maximize AUC only, between = convex combination"/> | |
82 <param name="conservative_fdr" argument="-algorithm:param_optimize:conservative_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use (D+1)/(T) instead of (D+1)/(T+D) for parameter estimation" help=""/> | |
83 </section> | |
84 </section> | |
85 <expand macro="adv_opts_macro"> | |
86 <param name="conservative_fdr" argument="-conservative_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use (D+1)/(T) instead of (D+1)/(T+D) for reporting protein FDRs" help=""/> | |
87 <param name="min_psms_extreme_probability" argument="-min_psms_extreme_probability" type="float" optional="true" value="0.0" label="Set PSMs with probability lower than this to this minimum probability" help=""/> | |
88 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | |
89 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
90 <expand macro="list_string_san"/> | |
91 </param> | |
92 </expand> | |
93 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
94 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
95 </param> | |
96 </inputs> | |
97 <outputs> | |
98 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> | |
99 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
100 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
101 </data> | |
102 </outputs> | |
103 <tests> | |
104 <expand macro="autotest_Epifany"/> | |
105 <expand macro="manutest_Epifany"/> | |
106 </tests> | |
107 <help><![CDATA[Runs a Bayesian protein inference. | |
108 | |
109 | |
110 For more information, visit http://www.openms.de/documentation/UTILS_Epifany.html]]></help> | |
111 <expand macro="references"/> | |
112 </tool> |