Mercurial > repos > galaxyp > openms_idrtcalibration

annotate IDRTCalibration.xml @ 14:7ff821b34ebc 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 19:25:24 +0000
parents 28805cf9b024
children f7226e34dc70
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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="IDRTCalibration" name="IDRTCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDRTCalibration</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($in.ext)' &&
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19 mkdir out &&
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21 ## Main program call
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23 set -o pipefail &&
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24 @EXECUTABLE@ -write_ctd ./ &&
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25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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27 -in
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28 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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29 -out
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30 'out/output.${gxy2omsext("idxml")}'
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31
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32 ## Postprocessing
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33 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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34 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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35 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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36 #end if]]></command>
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37 <configfiles>
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38 <inputs name="args_json" data_style="paths"/>
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39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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40 </configfiles>
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41 <inputs>
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42 <param argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/>
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43 <param argument="-calibrant_1_reference" type="float" optional="true" value="0.1" label="The RT of the first calibrant in the reference file" help=""/>
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44 <param argument="-calibrant_2_reference" type="float" optional="true" value="0.9" label="The RT of the second calibrant in the reference file" help=""/>
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45 <param argument="-calibrant_1_input" type="float" optional="true" value="-1.0" label="The RT of the first calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/>
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46 <param argument="-calibrant_2_input" type="float" optional="true" value="-1.0" label="The RT of the second calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/>
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47 <expand macro="adv_opts_macro">
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48 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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49 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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50 <expand macro="list_string_san" name="test"/>
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51 </param>
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52 </expand>
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53 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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54 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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55 </param>
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56 </inputs>
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57 <outputs>
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58 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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59 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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60 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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61 </data>
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62 </outputs>
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63 <tests><!-- TOPP_IDRTCalibration_1 -->
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64 <test expect_num_outputs="2">
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65 <section name="adv_opts">
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66 <param name="force" value="false"/>
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67 <param name="test" value="true"/>
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68 </section>
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69 <param name="in" value="IDRTCalibration_1_input.idXML"/>
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70 <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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71 <param name="calibrant_1_reference" value="0.1"/>
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72 <param name="calibrant_2_reference" value="0.9"/>
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73 <param name="calibrant_1_input" value="10.0"/>
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74 <param name="calibrant_2_input" value="90.0"/>
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75 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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76 <output name="ctd_out" ftype="xml">
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77 <assert_contents>
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78 <is_valid_xml/>
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79 </assert_contents>
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80 </output>
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81 </test>
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82 <!-- TOPP_IDRTCalibration_2 -->
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83 <test expect_num_outputs="2">
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84 <section name="adv_opts">
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85 <param name="force" value="false"/>
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86 <param name="test" value="true"/>
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87 </section>
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88 <param name="in" value="degenerated_empty.idXML"/>
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89 <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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90 <param name="calibrant_1_reference" value="0.1"/>
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91 <param name="calibrant_2_reference" value="0.9"/>
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92 <param name="calibrant_1_input" value="10.0"/>
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93 <param name="calibrant_2_input" value="90.0"/>
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94 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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95 <output name="ctd_out" ftype="xml">
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96 <assert_contents>
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97 <is_valid_xml/>
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98 </assert_contents>
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99 </output>
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100 </test>
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101 </tests>
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102 <help><![CDATA[Can be used to calibrate RTs of peptide hits linearly to standards.
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103
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104
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105 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRTCalibration.html]]></help>
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106 <expand macro="references"/>
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107 </tool>