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comparison FidoAdapter.xml @ 11:b552ec8456e7 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:09:56 +0000
parents d4965c549fd9
children c3a5cd016963
comparison
equal deleted inserted replaced
10:41859bbdc16e 11:b552ec8456e7
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="FidoAdapter" name="FidoAdapter" version="2.3.0"> 4 <tool id="FidoAdapter" name="FidoAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Runs the protein inference engine Fido.</description> 5 <description>Runs the protein inference engine Fido.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FidoAdapter</token> 7 <token name="@EXECUTABLE@">FidoAdapter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[FidoAdapter 15 @EXT_FOO@
14 -fidocp_executable FidoChooseParameters 16 #import re
15 -fido_executable Fido
16 17
17 #if $param_in: 18 ## Preprocessing
18 -in $param_in 19 mkdir in &&
19 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
20 #if $param_out: 21 mkdir out &&
21 -out $param_out 22
22 #end if 23 ## Main program call
23 #if $param_separate_runs: 24
24 -separate_runs 25 set -o pipefail &&
25 #end if 26 @EXECUTABLE@ -write_ctd ./ &&
26 #if $param_greedy_group_resolution: 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
27 -greedy_group_resolution 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
28 #end if 29 -in
29 #if $param_no_cleanup: 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
30 -no_cleanup 31 -out
31 #end if 32 'out/output.${gxy2omsext("idxml")}'
32 #if $param_all_PSMs: 33
33 -all_PSMs 34 ## Postprocessing
34 #end if 35 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
35 #if $param_group_level: 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
36 -group_level 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
37 #end if 38 #end if]]></command>
38 #if $param_log2_states: 39 <configfiles>
39 -log2_states $param_log2_states 40 <inputs name="args_json" data_style="paths"/>
40 #end if 41 <configfile name="hardcoded_json"><![CDATA[{"fido_executable": "Fido", "fidocp_executable": "FidoChooseParameters", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
41 #if $param_prob_protein: 42 </configfiles>
42 -prob:protein $param_prob_protein
43 #end if
44 #if $param_prob_peptide:
45 -prob:peptide $param_prob_peptide
46 #end if
47 #if $param_prob_spurious:
48 -prob:spurious $param_prob_spurious
49 #end if
50 #if $adv_opts.adv_opts_selector=='advanced':
51 #if $adv_opts.param_keep_zero_group:
52 -keep_zero_group
53 #end if
54 #if $adv_opts.param_accuracy:
55 -accuracy
56 #if " " in str($adv_opts.param_accuracy):
57 "$adv_opts.param_accuracy"
58 #else
59 $adv_opts.param_accuracy
60 #end if
61 #end if
62 #if $adv_opts.param_log2_states_precalc:
63 -log2_states_precalc $adv_opts.param_log2_states_precalc
64 #end if
65 #if $adv_opts.param_force:
66 -force
67 #end if
68 #end if
69 ]]></command>
70 <inputs> 43 <inputs>
71 <param name="param_in" type="data" format="idxml" optional="False" label="Input: identification results" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input: identification results" help=" select idxml data sets(s)"/>
72 <param name="param_separate_runs" display="radio" type="boolean" truevalue="-separate_runs" falsevalue="" checked="false" optional="True" label="Process multiple protein identification runs in the input separately, don't merge them" help="(-separate_runs) Merging results in loss of descriptive information of the single protein identification runs"/> 45 <param name="separate_runs" argument="-separate_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Process multiple protein identification runs in the input separately, don't merge them" help="Merging results in loss of descriptive information of the single protein identification runs"/>
73 <param name="param_greedy_group_resolution" display="radio" type="boolean" truevalue="-greedy_group_resolution" falsevalue="" checked="false" optional="True" label="Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities" help="(-greedy_group_resolution) Also adds the resolved ambiguity groups to output"/> 46 <param name="greedy_group_resolution" argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities" help="Also adds the resolved ambiguity groups to output"/>
74 <param name="param_no_cleanup" display="radio" type="boolean" truevalue="-no_cleanup" falsevalue="" checked="false" optional="True" label="Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)" help="(-no_cleanup) "/> 47 <param name="no_cleanup" argument="-no_cleanup" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)" help=""/>
75 <param name="param_all_PSMs" display="radio" type="boolean" truevalue="-all_PSMs" falsevalue="" checked="false" optional="True" label="Consider all PSMs of each peptide, instead of only the best one" help="(-all_PSMs) "/> 48 <param name="all_PSMs" argument="-all_PSMs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Consider all PSMs of each peptide, instead of only the best one" help=""/>
76 <param name="param_group_level" display="radio" type="boolean" truevalue="-group_level" falsevalue="" checked="false" optional="True" label="Perform inference on protein group level (instead of individual protein level)" help="(-group_level) This will lead to higher probabilities for (bigger) protein groups"/> 49 <param name="group_level" argument="-group_level" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform inference on protein group level (instead of individual protein level)" help="This will lead to higher probabilities for (bigger) protein groups"/>
77 <param name="param_log2_states" type="integer" min="0" optional="True" value="0" label="Binary logarithm of the max" help="(-log2_states) number of connected states in a subgraph. For a value N, subgraphs that are bigger than 2^N will be split up, sacrificing accuracy for runtime. '0' uses the default (18)"/> 50 <param name="log2_states" argument="-log2_states" type="integer" optional="true" min="0" value="0" label="Binary logarithm of the max" help="number of connected states in a subgraph. For a value N, subgraphs that are bigger than 2^N will be split up, sacrificing accuracy for runtime. '0' uses the default (18)"/>
78 <param name="param_prob_protein" type="float" min="0.0" optional="True" value="0.0" label="Protein prior probability ('gamma' parameter)" help="(-protein) "/> 51 <section name="prob" title="Probability values for running Fido directly" help="i.e. without parameter estimation (in which case other settings, except 'log2_states', are ignored)" expanded="false">
79 <param name="param_prob_peptide" type="float" min="0.0" optional="True" value="0.0" label="Peptide emission probability ('alpha' parameter)" help="(-peptide) "/> 52 <param name="protein" argument="-prob:protein" type="float" optional="true" min="0.0" value="0.0" label="Protein prior probability ('gamma' parameter)" help=""/>
80 <param name="param_prob_spurious" type="float" min="0.0" optional="True" value="0.0" label="Spurious peptide identification probability ('beta' parameter)" help="(-spurious) "/> 53 <param name="peptide" argument="-prob:peptide" type="float" optional="true" min="0.0" value="0.0" label="Peptide emission probability ('alpha' parameter)" help=""/>
81 <expand macro="advanced_options"> 54 <param name="spurious" argument="-prob:spurious" type="float" optional="true" min="0.0" value="0.0" label="Spurious peptide identification probability ('beta' parameter)" help=""/>
82 <param name="param_keep_zero_group" display="radio" type="boolean" truevalue="-keep_zero_group" falsevalue="" checked="false" optional="True" label="Keep the group of proteins with estimated probability of zero, which is otherwise removed (it may be very large)" help="(-keep_zero_group) "/> 55 </section>
83 <param name="param_accuracy" display="radio" type="select" optional="True" label="Accuracy level of start parameters" help="(-accuracy) There is a trade-off between accuracy and runtime. Empty uses the default ('best')"> 56 <expand macro="adv_opts_macro">
57 <param name="keep_zero_group" argument="-keep_zero_group" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep the group of proteins with estimated probability of zero, which is otherwise removed (it may be very large)" help=""/>
58 <param name="accuracy" argument="-accuracy" display="radio" type="select" optional="true" label="Accuracy level of start parameters" help="There is a trade-off between accuracy and runtime. Empty uses the default ('best')">
59 <option value="">default (nothing chosen)</option>
84 <option value=""></option> 60 <option value=""></option>
85 <option value="best">best</option> 61 <option value="best">best</option>
86 <option value="relaxed">relaxed</option> 62 <option value="relaxed">relaxed</option>
87 <option value="sloppy">sloppy</option> 63 <option value="sloppy">sloppy</option>
64 <expand macro="list_string_san"/>
88 </param> 65 </param>
89 <param name="param_log2_states_precalc" type="integer" min="0" optional="True" value="0" label="Like 'log2_states', but allows to set a separate limit for the precalculation" help="(-log2_states_precalc) "/> 66 <param name="log2_states_precalc" argument="-log2_states_precalc" type="integer" optional="true" min="0" value="0" label="Like 'log2_states', but allows to set a separate limit for the precalculation" help=""/>
90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 67 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
68 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
69 <expand macro="list_string_san"/>
70 </param>
91 </expand> 71 </expand>
72 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
73 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
74 </param>
92 </inputs> 75 </inputs>
93 <outputs> 76 <outputs>
94 <data name="param_out" format="idxml"/> 77 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
78 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
79 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
80 </data>
95 </outputs> 81 </outputs>
96 <help>Runs the protein inference engine Fido. 82 <tests>
83 <expand macro="autotest_FidoAdapter"/>
84 <expand macro="manutest_FidoAdapter"/>
85 </tests>
86 <help><![CDATA[Runs the protein inference engine Fido.
97 87
98 88
99 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FidoAdapter.html</help> 89 For more information, visit http://www.openms.de/documentation/TOPP_FidoAdapter.html]]></help>
90 <expand macro="references"/>
100 </tool> 91 </tool>