Mercurial > repos > galaxyp > openms_phosphoscoring

annotate PhosphoScoring.xml @ 13:996ca7c1d45e 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 19:08:12 +0000
parents c04ff2777ed2
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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="PhosphoScoring" name="PhosphoScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PhosphoScoring</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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16 ## Preprocessing
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 mkdir id &&
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20 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
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21 mkdir out &&
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23 ## Main program call
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24
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__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($in.ext)'
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31 -id
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32 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
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33 -out
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34 'out/output.${gxy2omsext("idxml")}'
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35
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36 ## Postprocessing
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37 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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38 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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39 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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40 #end if]]></command>
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41 <configfiles>
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42 <inputs name="args_json" data_style="paths"/>
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43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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44 </configfiles>
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45 <inputs>
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46 <param argument="-in" type="data" format="mzml" optional="false" label="Input file with MS/MS spectra" help=" select mzml data sets(s)"/>
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47 <param argument="-id" type="data" format="idxml" optional="false" label="Identification input file which contains a search against a concatenated sequence database" help=" select idxml data sets(s)"/>
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48 <param argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0" value="0.05" label="Fragment mass tolerance for spectrum comparisons" help=""/>
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49 <param argument="-fragment_mass_unit" type="select" optional="true" label="Unit of fragment mass tolerance" help="">
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50 <option value="Da" selected="true">Da</option>
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51 <option value="ppm">ppm</option>
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52 <expand macro="list_string_san" name="fragment_mass_unit"/>
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53 </param>
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54 <expand macro="adv_opts_macro">
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55 <param argument="-max_peptide_length" type="integer" optional="true" min="0" value="40" label="Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')" help=""/>
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56 <param argument="-max_num_perm" type="integer" optional="true" min="0" value="16384" label="Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')" help=""/>
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57 <param argument="-unambiguous_score" type="integer" optional="true" value="1000" label="Score to use for unambiguous assignments, where all sites on a peptide are phosphorylated" help="(Note: If a peptide is not phosphorylated at all, its score is set to '-1'.)"/>
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58 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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59 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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60 <expand macro="list_string_san" name="test"/>
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61 </param>
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62 </expand>
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63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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65 </param>
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66 </inputs>
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67 <outputs>
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68 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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71 </data>
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72 </outputs>
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73 <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
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74 <param name="adv_opts|test" value="true"/>
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75 <param name="in" ftype="mzml" value="spectra.mzML"/>
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76 <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
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77 <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
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78 </test>
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79 </tests>
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80 <help><![CDATA[Scores potential phosphorylation sites in order to localize the most probable sites.
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82
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83 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PhosphoScoring.html]]></help>
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84 <expand macro="references"/>
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85 </tool>