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annotate FileInfo.xml @ 11:98f171dab07c 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 12:52:57 +0000
parents 92922182d423
children e8dce5e07fa5
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a5e996f13660 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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: [File Handling]-->
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4 <tool id="FileInfo" name="FileInfo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Shows basic information about the file, such as data ranges and file type.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FileInfo</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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17
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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($in.ext)' &&
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21 mkdir out &&
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22 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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23 mkdir out_tsv &&
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24 #end if
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26 ## Main program call
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28 set -o pipefail &&
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29 @EXECUTABLE@ -write_ctd ./ &&
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30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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32 -in
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33 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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34 -out
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35 'out/output.${gxy2omsext("txt")}'
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36 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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37 -out_tsv
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38 'out_tsv/output.${gxy2omsext("csv")}'
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39 #end if
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40 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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41 | tee '$stdout'
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42 #end if
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44 ## Postprocessing
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45 && mv 'out/output.${gxy2omsext("txt")}' '$out'
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46 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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47 && mv 'out_tsv/output.${gxy2omsext("csv")}' '$out_tsv'
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48 #end if
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49 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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50 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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51 #end if]]></command>
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52 <configfiles>
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53 <inputs name="args_json" data_style="paths"/>
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54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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55 </configfiles>
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56 <inputs>
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57 <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,trafoxml" optional="false" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,trafoxml data sets(s)"/>
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58 <param name="m" argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
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59 <param name="p" argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
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60 <param name="s" argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/>
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61 <param name="d" argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/>
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62 <param name="c" argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/>
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63 <param name="v" argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/>
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64 <param name="i" argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/>
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65 <expand macro="adv_opts_macro">
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66 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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67 <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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68 <expand macro="list_string_san"/>
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69 </param>
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70 </expand>
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71 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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72 <option value="out_tsv_FLAG">out_tsv (Enables the test mode (needed for internal use only))</option>
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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 ${on_string}: out" format="txt"/>
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78 <data name="out_tsv" label="${tool.name} on ${on_string}: out_tsv" format="csv">
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79 <filter>OPTIONAL_OUTPUTS is not None and "out_tsv_FLAG" in OPTIONAL_OUTPUTS</filter>
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80 </data>
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81 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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82 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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83 </data>
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84 </outputs>
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85 <tests>
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86 <expand macro="autotest_FileInfo"/>
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87 <expand macro="manutest_FileInfo"/>
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88 </tests>
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89 <help><![CDATA[Shows basic information about the file, such as data ranges and file type.
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90
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91
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92 For more information, visit http://www.openms.de/documentation/TOPP_FileInfo.html]]></help>
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93 <expand macro="references"/>
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94 </tool>