Mercurial > repos > galaxyp > openms_masscalculator

annotate MassCalculator.xml @ 11:65c6e741ddf3 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:13:07 +0000
parents ff18cb79cdd2
children bcd50cd4fe42
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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: [Utilities]-->
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4 <tool id="MassCalculator" name="MassCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MassCalculator</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 #if $in:
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20 mkdir in &&
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21 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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22 #end if
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23 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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24 mkdir out &&
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25 #end if
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27 ## Main program call
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29 set -o pipefail &&
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30 @EXECUTABLE@ -write_ctd ./ &&
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31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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33 #if $in:
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34 -in
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35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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36 #end if
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37 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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38 -out
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39 'out/output.${gxy2omsext("csv")}'
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40 #end if
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41 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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42 | tee '$stdout'
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43 #end if
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45 ## Postprocessing
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46 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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47 && mv 'out/output.${gxy2omsext("csv")}' '$out'
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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="tabular" optional="true" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select tabular data sets(s)"/>
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58 <param name="in_seq" argument="-in_seq" type="text" optional="true" value="" label="List of peptide sequences (mutually exclusive to 'in')" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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59 <expand macro="list_string_val"/>
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60 <expand macro="list_string_san"/>
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61 </param>
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62 <param name="charge" argument="-charge" type="text" optional="true" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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63 <expand macro="list_integer_valsan"/>
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64 </param>
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65 <param name="format" argument="-format" display="radio" type="select" optional="false" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="">
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66 <option value="list" selected="true">list</option>
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67 <option value="table">table</option>
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68 <option value="mass_only">mass_only</option>
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69 <option value="mz_only">mz_only</option>
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70 <expand macro="list_string_san"/>
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71 </param>
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72 <param name="average_mass" argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) peptide masses" help=""/>
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73 <param name="fragment_type" argument="-fragment_type" type="select" optional="false" label="For what type of sequence/fragment the mass should be computed" help="">
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74 <option value="full" selected="true">full</option>
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75 <option value="internal">internal</option>
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76 <option value="N-terminal">N-terminal</option>
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77 <option value="C-terminal">C-terminal</option>
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78 <option value="a-ion">a-ion</option>
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79 <option value="b-ion">b-ion</option>
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80 <option value="c-ion">c-ion</option>
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81 <option value="x-ion">x-ion</option>
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82 <option value="y-ion">y-ion</option>
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83 <option value="z-ion">z-ion</option>
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84 <expand macro="list_string_san"/>
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85 </param>
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86 <param name="separator" argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="">
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87 <expand macro="list_string_san"/>
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88 </param>
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89 <expand macro="adv_opts_macro">
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90 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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91 <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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92 <expand macro="list_string_san"/>
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93 </param>
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94 </expand>
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95 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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96 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option>
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97 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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98 </param>
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99 </inputs>
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100 <outputs>
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101 <data name="out" label="${tool.name} on ${on_string}: out" format="csv">
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102 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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103 </data>
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104 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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105 <filter>OPTIONAL_OUTPUTS is None</filter>
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106 </data>
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107 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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108 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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109 </data>
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110 </outputs>
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111 <tests>
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112 <expand macro="autotest_MassCalculator"/>
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113 <expand macro="manutest_MassCalculator"/>
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114 </tests>
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115 <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences
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116
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117
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118 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MassCalculator.html]]></help>
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119 <expand macro="references"/>
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120 </tool>