annotate MassCalculator.xml @ 13:bcd50cd4fe42 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:08:33 +0000
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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@VERSION_SUFFIX@" profile="21.05">
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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 </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 #if $in:
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18 mkdir in &&
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19 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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20 #end if
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21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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22 mkdir out &&
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23 #end if
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24
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25 ## Main program call
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27 set -o pipefail &&
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28 @EXECUTABLE@ -write_ctd ./ &&
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29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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31 #if $in:
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32 -in
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33 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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34 #end if
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35 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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36 -out
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37 'out/output.${gxy2omsext("csv")}'
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38 #end if
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39 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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40 | tee '$stdout'
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41 #end if
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43 ## Postprocessing
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44 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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45 && mv 'out/output.${gxy2omsext("csv")}' '$out'
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46 #end if
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47 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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48 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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49 #end if]]></command>
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50 <configfiles>
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51 <inputs name="args_json" data_style="paths"/>
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52 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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53 </configfiles>
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54 <inputs>
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55 <param 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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56 <param 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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57 <expand macro="list_string_val" name="in_seq"/>
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58 <expand macro="list_string_san" name="in_seq"/>
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59 </param>
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60 <param 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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61 <expand macro="list_integer_valsan" name="charge"/>
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62 </param>
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63 <param argument="-format" type="select" optional="true" 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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64 <option value="list" selected="true">list</option>
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65 <option value="table">table</option>
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66 <option value="mass_only">mass_only</option>
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67 <option value="mz_only">mz_only</option>
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68 <expand macro="list_string_san" name="format"/>
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69 </param>
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70 <param argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) peptide masses" help=""/>
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71 <param argument="-fragment_type" type="select" optional="true" label="For what type of sequence/fragment the mass should be computed" help="">
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72 <option value="full" selected="true">full</option>
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73 <option value="internal">internal</option>
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74 <option value="N-terminal">N-terminal</option>
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75 <option value="C-terminal">C-terminal</option>
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76 <option value="a-ion">a-ion</option>
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77 <option value="b-ion">b-ion</option>
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78 <option value="c-ion">c-ion</option>
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79 <option value="x-ion">x-ion</option>
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80 <option value="y-ion">y-ion</option>
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81 <option value="z-ion">z-ion</option>
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82 <expand macro="list_string_san" name="fragment_type"/>
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83 </param>
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84 <param 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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85 <expand macro="list_string_san" name="separator"/>
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86 </param>
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87 <expand macro="adv_opts_macro">
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88 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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89 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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90 <expand macro="list_string_san" name="test"/>
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91 </param>
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92 </expand>
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93 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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94 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option>
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95 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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96 </param>
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97 </inputs>
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98 <outputs>
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99 <data name="out" label="${tool.name} on ${on_string}: out" format="csv">
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100 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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101 </data>
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102 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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103 <filter>OPTIONAL_OUTPUTS is None</filter>
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104 </data>
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105 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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106 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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107 </data>
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108 </outputs>
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109 <tests><!-- UTILS_MassCalculator_1 -->
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110 <test expect_num_outputs="2">
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111 <section name="adv_opts">
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112 <param name="force" value="false"/>
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113 <param name="test" value="true"/>
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114 </section>
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115 <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/>
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116 <param name="in_seq" value=""/>
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117 <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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118 <param name="charge" value="0 1"/>
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119 <param name="format" value="table"/>
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120 <param name="average_mass" value="false"/>
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121 <param name="fragment_type" value="full"/>
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122 <param name="separator" value=","/>
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123 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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124 <output name="ctd_out" ftype="xml">
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125 <assert_contents>
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126 <is_valid_xml/>
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127 </assert_contents>
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128 </output>
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129 </test>
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130 <!-- UTILS_MassCalculator_2 -->
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131 <test expect_num_outputs="2">
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132 <section name="adv_opts">
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133 <param name="force" value="false"/>
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134 <param name="test" value="true"/>
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135 </section>
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136 <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
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137 <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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138 <param name="charge" value="1 2 3"/>
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139 <param name="format" value="list"/>
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140 <param name="average_mass" value="false"/>
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141 <param name="fragment_type" value="full"/>
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142 <param name="separator" value=""/>
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143 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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144 <output name="ctd_out" ftype="xml">
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145 <assert_contents>
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146 <is_valid_xml/>
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147 </assert_contents>
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148 </output>
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149 </test>
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150 </tests>
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151 <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences
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152
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153
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154 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MassCalculator.html]]></help>
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155 <expand macro="references"/>
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156 </tool>