Mercurial > repos > galaxyp > openms_openswathassaygenerator

annotate OpenSwathAssayGenerator.xml @ 9:5848492bfc5a 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 12:44:29 +0000
parents 63a26a130c5d
children a41cd777ced9
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c5136f02a0fa 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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462eb95f7382 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Generates assays according to different models for a specific TraML</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathAssayGenerator</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 $swath_windows_file:
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23 mkdir swath_windows_file &&
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24 ln -s '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
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25 #end if
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26 #if $unimod_file:
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27 mkdir unimod_file &&
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28 ln -s '$unimod_file' 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)' &&
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29 #end if
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5848492bfc5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 ## Main program call
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33 set -o pipefail &&
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34 @EXECUTABLE@ -write_ctd ./ &&
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35 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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36 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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37 -in
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38 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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39 -out
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40 'out/output.${out_type}'
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41 #if $swath_windows_file:
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42 -swath_windows_file
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43 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)'
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44 #end if
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45 #if $unimod_file:
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46 -unimod_file
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47 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)'
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48 #end if
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49
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50 ## Postprocessing
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51 && mv 'out/output.${out_type}' '$out'
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52 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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53 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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54 #end if]]></command>
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55 <configfiles>
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56 <inputs name="args_json" data_style="paths"/>
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57 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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58 </configfiles>
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59 <inputs>
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60 <param name="in" argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
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61 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
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62 <option value="TraML">traml</option>
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63 <option value="pqp">pqp</option>
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64 <option value="tsv">tabular (tsv)</option>
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65 <expand macro="list_string_san"/>
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66 </param>
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67 <param name="min_transitions" argument="-min_transitions" type="integer" optional="true" value="6" label="minimal number of transitions" help=""/>
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68 <param name="max_transitions" argument="-max_transitions" type="integer" optional="true" value="6" label="maximal number of transitions" help=""/>
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69 <param name="allowed_fragment_types" argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help="">
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70 <expand macro="list_string_san"/>
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71 </param>
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72 <param name="allowed_fragment_charges" argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help="">
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73 <expand macro="list_string_san"/>
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74 </param>
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75 <param name="enable_detection_specific_losses" argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
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76 <param name="enable_detection_unspecific_losses" argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
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77 <param name="precursor_mz_threshold" argument="-precursor_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/>
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78 <param name="precursor_lower_mz_limit" argument="-precursor_lower_mz_limit" type="float" optional="true" value="400.0" label="lower MZ limit for precursor ions" help=""/>
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79 <param name="precursor_upper_mz_limit" argument="-precursor_upper_mz_limit" type="float" optional="true" value="1200.0" label="upper MZ limit for precursor ions" help=""/>
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80 <param name="product_mz_threshold" argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
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81 <param name="product_lower_mz_limit" argument="-product_lower_mz_limit" type="float" optional="true" value="350.0" label="lower MZ limit for fragment ions" help=""/>
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82 <param name="product_upper_mz_limit" argument="-product_upper_mz_limit" type="float" optional="true" value="2000.0" label="upper MZ limit for fragment ions" help=""/>
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83 <param name="swath_windows_file" argument="-swath_windows_file" type="data" format="txt" optional="true" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
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84 <param name="unimod_file" argument="-unimod_file" type="data" format="xml" optional="true" label="(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability" help=" select xml data sets(s)"/>
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85 <param name="enable_ipf" argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions should be generated for IPF" help="Note: Requires setting 'unimod_file'"/>
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86 <expand macro="adv_opts_macro">
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87 <param name="max_num_alternative_localizations" argument="-max_num_alternative_localizations" type="integer" optional="true" value="10000" label="IPF: maximum number of site-localization permutations" help=""/>
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88 <param name="disable_identification_ms2_precursors" argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/>
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89 <param name="disable_identification_specific_losses" argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/>
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90 <param name="enable_identification_unspecific_losses" argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/>
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91 <param name="enable_swath_specifity" argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/>
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92 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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93 <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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94 <expand macro="list_string_san"/>
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95 </param>
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96 </expand>
9
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97 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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98 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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99 </param>
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100 </inputs>
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101 <outputs>
9
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102 <data name="out" label="${tool.name} on ${on_string}: out">
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103 <change_format>
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104 <when input="out_type" value="TraML" format="traml"/>
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105 <when input="out_type" value="pqp" format="pqp"/>
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106 <when input="out_type" value="tsv" format="tabular"/>
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107 </change_format>
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108 </data>
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109 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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110 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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111 </data>
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112 </outputs>
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113 <tests>
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114 <expand macro="autotest_OpenSwathAssayGenerator"/>
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115 <expand macro="manutest_OpenSwathAssayGenerator"/>
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116 </tests>
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117 <help><![CDATA[Generates assays according to different models for a specific TraML
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118
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119
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120 For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathAssayGenerator.html]]></help>
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121 <expand macro="references"/>
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122 </tool>