Mercurial > repos > galaxyp > openms_fidoadapter

annotate FidoAdapter.xml @ 12:39a1dd32a40d draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
author galaxyp
date Wed, 23 Sep 2020 14:58:55 +0000
parents b552ec8456e7
children c3a5cd016963
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="FidoAdapter" name="FidoAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Runs the protein inference engine Fido.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FidoAdapter</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir out &&
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23 ## Main program call
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 -out
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32 'out/output.${gxy2omsext("idxml")}'
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33
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34 ## Postprocessing
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35 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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38 #end if]]></command>
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39 <configfiles>
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40 <inputs name="args_json" data_style="paths"/>
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41 <configfile name="hardcoded_json"><![CDATA[{"fido_executable": "Fido", "fidocp_executable": "FidoChooseParameters", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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42 </configfiles>
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43 <inputs>
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44 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input: identification results" help=" select idxml data sets(s)"/>
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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"/>
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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"/>
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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=""/>
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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=""/>
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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"/>
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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)"/>
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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">
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52 <param name="protein" argument="-prob:protein" type="float" optional="true" min="0.0" value="0.0" label="Protein prior probability ('gamma' parameter)" help=""/>
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53 <param name="peptide" argument="-prob:peptide" type="float" optional="true" min="0.0" value="0.0" label="Peptide emission probability ('alpha' parameter)" help=""/>
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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=""/>
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55 </section>
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56 <expand macro="adv_opts_macro">
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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=""/>
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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')">
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59 <option value="">default (nothing chosen)</option>
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60 <option value=""></option>
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61 <option value="best">best</option>
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62 <option value="relaxed">relaxed</option>
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63 <option value="sloppy">sloppy</option>
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64 <expand macro="list_string_san"/>
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65 </param>
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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=""/>
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67 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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68 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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69 <expand macro="list_string_san"/>
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70 </param>
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71 </expand>
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72 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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73 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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74 </param>
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75 </inputs>
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76 <outputs>
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77 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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78 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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79 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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80 </data>
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81 </outputs>
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82 <tests>
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83 <expand macro="autotest_FidoAdapter"/>
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84 <expand macro="manutest_FidoAdapter"/>
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85 </tests>
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86 <help><![CDATA[Runs the protein inference engine Fido.
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87
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88
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89 For more information, visit http://www.openms.de/documentation/TOPP_FidoAdapter.html]]></help>
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90 <expand macro="references"/>
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91 </tool>