Mercurial > repos > galaxyp > openms_openswathdiaprescoring

annotate OpenSwathDIAPreScoring.xml @ 11:c99d5004b74f draft

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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 19:20:01 +0000
parents e6ba7a995b35
children 986d14ec9394
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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: [Targeted Experiments]-->
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4 <tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Scoring spectra using the DIA scores.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</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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15
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16 ## Preprocessing
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17 mkdir tr &&
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18 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
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19 mkdir swath_files_cond.swath_files &&
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20 #if $swath_files_cond.swath_files_select == "no"
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21 mkdir ${' '.join(["'swath_files_cond.swath_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} &&
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22 ${' '.join(["ln -s '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
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23 #else
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24 ln -s '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' &&
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25 #end if
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26 mkdir output_files &&
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27 mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} &&
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29 ## Main program call
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31 set -o pipefail &&
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32 @EXECUTABLE@ -write_ctd ./ &&
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33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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35 -tr
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36 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
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37 -swath_files
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38 #if $swath_files_cond.swath_files_select == "no"
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39 ${' '.join(["'swath_files_cond.swath_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
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40 #else
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41 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)'
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42 #end if
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43 -output_files
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44 ${' '.join(["'output_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("tabular")) for i, f in enumerate($swath_files_cond.swath_files) if f])}
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45
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46 ## Postprocessing
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47 ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(gext)s' 'output_files/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("tabular")} for i, f in enumerate($swath_files_cond.swath_files) if f])}
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48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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49 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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50 #end if]]></command>
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51 <configfiles>
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52 <inputs name="args_json" data_style="paths"/>
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53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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54 </configfiles>
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55 <inputs>
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56 <param argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
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57 <conditional name="swath_files_cond">
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58 <param name="swath_files_select" type="select" label="Run tool in batch mode for -swath_files">
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59 <option value="no">No: process all datasets jointly</option>
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60 <option value="yes">Yes: process each dataset in an independent job</option>
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61 </param>
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62 <when value="no">
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63 <param argument="-swath_files" type="data" format="mzml" multiple="true" optional="false" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
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64 </when>
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65 <when value="yes">
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66 <param argument="-swath_files" type="data" format="mzml" multiple="false" optional="false" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
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67 </when>
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68 </conditional>
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69 <param argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/>
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70 <expand macro="adv_opts_macro">
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71 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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72 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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73 <expand macro="list_string_san" name="test"/>
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74 </param>
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75 </expand>
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76 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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77 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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78 </param>
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79 </inputs>
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80 <outputs>
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81 <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">
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82 <discover_datasets directory="output_files" recurse="true" format="tabular" pattern="__name__"/>
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83 </collection>
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84 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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85 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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86 </data>
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87 </outputs>
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88 <tests><!-- data from a test that included all the needed test files -->
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89 <test>
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90 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
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91 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
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92 <output_collection name="output_files" count="1">
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93 <element name="OpenSwathAnalyzer_2_swathfile_mzML" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
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94 </output_collection>
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95 </test>
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96 <!-- test with two inputs (actually the same file .. symlinked) -->
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97 <test>
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98 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
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99 <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
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100 <output_collection name="output_files" count="2">
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101 <element name="OpenSwathDIAPreScoring_in1_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/>
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102 <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/>
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103 </output_collection>
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104 </test>
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105 </tests>
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106 <help><![CDATA[Scoring spectra using the DIA scores.
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107
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108
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109 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathDIAPreScoring.html]]></help>
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110 <expand macro="references"/>
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111 </tool>