Mercurial > repos > galaxyp > openms_epifany
comparison Epifany.xml @ 2:16cdef222ea2 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author | galaxyp |
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date | Tue, 13 Oct 2020 19:45:31 +0000 |
parents | 03e13b23a78b |
children | f3096a586de8 |
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1:015b55cd3570 | 2:16cdef222ea2 |
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16 #import re | 16 #import re |
17 | 17 |
18 ## Preprocessing | 18 ## Preprocessing |
19 mkdir in && | 19 mkdir in && |
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } | 20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } |
21 #if $exp_design: | |
22 mkdir exp_design && | |
23 ln -s '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' && | |
24 #end if | |
21 mkdir out && | 25 mkdir out && |
22 | 26 |
23 ## Main program call | 27 ## Main program call |
24 | 28 |
25 set -o pipefail && | 29 set -o pipefail && |
26 @EXECUTABLE@ -write_ctd ./ && | 30 @EXECUTABLE@ -write_ctd ./ && |
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | 31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | 32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
29 -in | 33 -in |
30 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | 34 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} |
35 #if $exp_design: | |
36 -exp_design | |
37 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' | |
38 #end if | |
31 -out | 39 -out |
32 'out/output.${gxy2omsext("idxml")}' | 40 'out/output.${out_type}' |
33 | 41 |
34 ## Postprocessing | 42 ## Postprocessing |
35 && mv 'out/output.${gxy2omsext("idxml")}' '$out' | 43 && mv 'out/output.${out_type}' '$out' |
36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS | 44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
37 && mv '@EXECUTABLE@.ctd' '$ctd_out' | 45 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
38 #end if]]></command> | 46 #end if]]></command> |
39 <configfiles> | 47 <configfiles> |
40 <inputs name="args_json" data_style="paths"/> | 48 <inputs name="args_json" data_style="paths"/> |
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
42 </configfiles> | 50 </configfiles> |
43 <inputs> | 51 <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)"/> | 52 <param name="in" argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="false" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/> |
53 <param name="exp_design" argument="-exp_design" type="data" format="tabular" optional="true" label="(Currently unused) Input: experimental design" help=" select tabular data sets(s)"/> | |
54 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output type: auto detected by file extension but can be overwritten here" help=""> | |
55 <option value="consensusXML">consensusxml</option> | |
56 <option value="idXML">idxml</option> | |
57 <expand macro="list_string_san"/> | |
58 </param> | |
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=""/> | 59 <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"> | 60 <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> | 61 <option value="none" selected="true">none</option> |
48 <option value="remove_associations_only">remove_associations_only</option> | 62 <option value="remove_associations_only">remove_associations_only</option> |
49 <option value="remove_proteins_wo_evidence">remove_proteins_wo_evidence</option> | 63 <option value="remove_proteins_wo_evidence">remove_proteins_wo_evidence</option> |
50 <expand macro="list_string_san"/> | 64 <expand macro="list_string_san"/> |
51 </param> | 65 </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=""/> | 66 <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"> | 67 <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=""/> | 68 <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 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"/> | 69 <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"/> |
70 <param name="keep_best_PSM_only" argument="-algorithm:keep_best_PSM_only" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Epifany uses the best PSM per peptide for inference" help="Discard the rest (true) or keepe.g. for quantification/reporting?"/> | |
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=""/> | 71 <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=""/> | 72 <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=""/> | 73 <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=""/> | 74 <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"> | 75 <section name="model_parameters" title="Model parameters for the Bayesian network" help="" expanded="false"> |
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=""/> | 79 <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=""/> | 80 <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=""/> | 81 <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> | 82 </section> |
68 <section name="loopy_belief_propagation" title="Settings for the loopy belief propagation algorithm" help="" expanded="false"> | 83 <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"> | 84 <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. subtree = message passing follows a random spanning tree in each iteration"> |
70 <option value="priority" selected="true">priority</option> | 85 <option value="priority" selected="true">priority</option> |
71 <option value="fifo">fifo</option> | 86 <option value="fifo">fifo</option> |
72 <option value="random_spanning_tree">random_spanning_tree</option> | 87 <option value="subtree">subtree</option> |
73 <expand macro="list_string_san"/> | 88 <expand macro="list_string_san"/> |
74 </param> | 89 </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=""/> | 90 <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"/> | 91 <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=""/> | 92 <param name="max_nr_iterations" argument="-algorithm:loopy_belief_propagation:max_nr_iterations" type="integer" optional="true" value="2147483647" label="(Usually auto-determined by estimated but you can set a hard limit here)" help="If not all messages converge, how many iterations should be done at max per connected component?"/> |
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"/> | 93 <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> | 94 </section> |
80 <section name="param_optimize" title="Settings for the parameter optimization" help="" expanded="false"> | 95 <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"/> | 96 <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 target decoy 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=""/> | 97 <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=""/> |
98 <param name="regularized_fdr" argument="-algorithm:param_optimize:regularized_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use a regularized FDR for proteins without unique peptides" help=""/> | |
83 </section> | 99 </section> |
84 </section> | 100 </section> |
85 <expand macro="adv_opts_macro"> | 101 <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=""/> | 102 <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=""/> | 103 <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=""/> | 104 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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=""> | 105 <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"/> | 106 <expand macro="list_string_san"/> |
91 </param> | 107 </param> |
92 </expand> | 108 </expand> |
93 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | 109 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
94 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 110 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
95 </param> | 111 </param> |
96 </inputs> | 112 </inputs> |
97 <outputs> | 113 <outputs> |
98 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> | 114 <data name="out" label="${tool.name} on ${on_string}: out"> |
115 <change_format> | |
116 <when input="out_type" value="consensusXML" format="consensusxml"/> | |
117 <when input="out_type" value="idXML" format="idxml"/> | |
118 </change_format> | |
119 </data> | |
99 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 120 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
100 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 121 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
101 </data> | 122 </data> |
102 </outputs> | 123 </outputs> |
103 <tests> | 124 <tests> |
105 <expand macro="manutest_Epifany"/> | 126 <expand macro="manutest_Epifany"/> |
106 </tests> | 127 </tests> |
107 <help><![CDATA[Runs a Bayesian protein inference. | 128 <help><![CDATA[Runs a Bayesian protein inference. |
108 | 129 |
109 | 130 |
110 For more information, visit http://www.openms.de/documentation/UTILS_Epifany.html]]></help> | 131 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_Epifany.html]]></help> |
111 <expand macro="references"/> | 132 <expand macro="references"/> |
112 </tool> | 133 </tool> |