Mercurial > repos > galaxyp > openms_rnamasscalculator

annotate RNAMassCalculator.xml @ 5:148c000ea2ec draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:33:05 +0000
parents cb0f5beef55f
children
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4f8478024146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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1 <!--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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148c000ea2ec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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2 <!--Proposed Tool Section: [RNA]-->
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3 <tool id="RNAMassCalculator" name="RNAMassCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">RNAMassCalculator</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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4f8478024146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 ## Preprocessing
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16 #if $in:
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17 mkdir in &&
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148c000ea2ec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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18 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 #end if
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20 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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21 mkdir out &&
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22 #end if
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4f8478024146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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24 ## Main program call
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4f8478024146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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26 set -o pipefail &&
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27 @EXECUTABLE@ -write_ctd ./ &&
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28 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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29 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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30 #if $in:
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31 -in
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32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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33 #end if
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34 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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35 -out
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36 'out/output.${gxy2omsext("txt")}'
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37 #end if
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38 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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39 | tee '$stdout'
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40 #end if
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41
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42 ## Postprocessing
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43 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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44 && mv 'out/output.${gxy2omsext("txt")}' '$out'
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45 #end if
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46 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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47 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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48 #end if]]></command>
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49 <configfiles>
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50 <inputs name="args_json" data_style="paths"/>
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51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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52 </configfiles>
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53 <inputs>
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54 <param argument="-in" type="data" format="txt" optional="true" label="Input file with RNA sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select txt data sets(s)"/>
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55 <param argument="-in_seq" type="text" optional="true" value="" label="List of RNA 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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56 <expand macro="list_string_val" name="in_seq"/>
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57 <expand macro="list_string_san" name="in_seq"/>
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58 </param>
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59 <param argument="-charge" type="text" 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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60 <expand macro="list_integer_valsan" name="charge"/>
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61 </param>
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62 <param argument="-format" type="select" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only, 'formula_only': sum formula only)" help="">
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63 <option value="list" selected="true">list</option>
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64 <option value="table">table</option>
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65 <option value="mass_only">mass_only</option>
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66 <option value="mz_only">mz_only</option>
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67 <option value="formula_only">formula_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) oligonucleotide masses" help=""/>
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71 <param argument="-fragment_type" type="select" 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="5-prime">5-prime</option>
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75 <option value="3-prime">3-prime</option>
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76 <option value="a-B-ion">a-B-ion</option>
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77 <option value="a-ion">a-ion</option>
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78 <option value="b-ion">b-ion</option>
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79 <option value="c-ion">c-ion</option>
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80 <option value="d-ion">d-ion</option>
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81 <option value="w-ion">w-ion</option>
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82 <option value="x-ion">x-ion</option>
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83 <option value="y-ion">y-ion</option>
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84 <option value="z-ion">z-ion</option>
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85 <expand macro="list_string_san" name="fragment_type"/>
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86 </param>
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87 <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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88 <expand macro="list_string_san" name="separator"/>
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89 </param>
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90 <expand macro="adv_opts_macro">
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91 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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92 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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93 <expand macro="list_string_san" name="test"/>
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94 </param>
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95 </expand>
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96 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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97 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option>
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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>
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102 <data name="out" label="${tool.name} on ${on_string}: out" format="txt">
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103 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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104 </data>
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105 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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106 <filter>OPTIONAL_OUTPUTS is None</filter>
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107 </data>
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108 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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109 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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110 </data>
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111 </outputs>
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112 <tests>
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113 <!-- TOPP_RNAMassCalculator_1 -->
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114 <test expect_num_outputs="2">
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115 <section name="adv_opts">
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116 <param name="force" value="false"/>
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117 <param name="test" value="true"/>
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118 </section>
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119 <param name="in_seq" value="&quot;AUCGGC&quot;"/>
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120 <output name="out" value="RNAMassCalculator_1.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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121 <param name="charge" value="-1 -2"/>
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122 <param name="format" value="list"/>
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123 <param name="average_mass" value="false"/>
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124 <param name="fragment_type" value="full"/>
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125 <param name="separator" value=""/>
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126 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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127 <output name="ctd_out" ftype="xml">
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128 <assert_contents>
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129 <is_valid_xml/>
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130 </assert_contents>
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131 </output>
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132 <assert_stdout>
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133 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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134 </assert_stdout>
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135 </test>
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136 </tests>
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137 <help><![CDATA[Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences
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138
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139
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140 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNAMassCalculator.html]]></help>
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141 <expand macro="references"/>
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142 </tool>