Mercurial > repos > galaxyp > openms_databasefilter

annotate DatabaseFilter.xml @ 15:2f7a8b58314e 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 21:44:52 +0000
parents 0878a55de9e7
children
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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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2 <!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
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3 <tool id="DatabaseFilter" name="DatabaseFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Filters a protein database (FASTA format) based on identified proteins</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">DatabaseFilter</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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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir id &&
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19 cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
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20 mkdir out &&
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22 ## Main program call
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24 set -o pipefail &&
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25 @EXECUTABLE@ -write_ctd ./ &&
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26 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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27 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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28 -in
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29 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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30 -id
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31 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
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32 -out
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33 'out/output.${gxy2omsext("fasta")}'
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35 ## Postprocessing
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36 && mv 'out/output.${gxy2omsext("fasta")}' '$out'
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37 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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38 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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39 #end if]]></command>
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40 <configfiles>
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41 <inputs name="args_json" data_style="paths"/>
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42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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43 </configfiles>
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44 <inputs>
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45 <param argument="-in" type="data" format="fasta" label="Input FASTA file, containing a database" help=" select fasta data sets(s)"/>
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46 <param argument="-id" type="data" format="idxml,mzid" label="Input file containing identified peptides and proteins" help=" select idxml,mzid data sets(s)"/>
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47 <param argument="-method" type="select" label="Switch between white-/blacklisting" help="">
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48 <option value="whitelist" selected="true">whitelist</option>
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49 <option value="blacklist">blacklist</option>
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50 <expand macro="list_string_san" name="method"/>
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51 </param>
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52 <expand macro="adv_opts_macro">
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53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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54 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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55 <expand macro="list_string_san" name="test"/>
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56 </param>
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57 </expand>
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58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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60 </param>
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61 </inputs>
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62 <outputs>
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63 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/>
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64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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66 </data>
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67 </outputs>
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68 <tests>
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69 <!-- TOPP_DatabaseFilter_1 -->
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70 <test expect_num_outputs="2">
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71 <section name="adv_opts">
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72 <param name="force" value="false"/>
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73 <param name="test" value="true"/>
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74 </section>
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75 <param name="in" value="DatabaseFilter_1.fasta"/>
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76 <param name="id" value="DatabaseFilter_1.idXML"/>
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77 <param name="method" value="whitelist"/>
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78 <output name="out" value="DatabaseFilter_1_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
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79 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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80 <output name="ctd_out" ftype="xml">
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81 <assert_contents>
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82 <is_valid_xml/>
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83 </assert_contents>
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84 </output>
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85 <assert_stdout>
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86 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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87 </assert_stdout>
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88 </test>
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89 <!-- TOPP_DatabaseFilter_2 -->
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90 <test expect_num_outputs="2">
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91 <section name="adv_opts">
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92 <param name="force" value="false"/>
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93 <param name="test" value="true"/>
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94 </section>
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95 <param name="in" value="DatabaseFilter_1.fasta"/>
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96 <param name="id" value="DatabaseFilter_1.idXML"/>
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97 <param name="method" value="blacklist"/>
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98 <output name="out" value="DatabaseFilter_2_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
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99 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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100 <output name="ctd_out" ftype="xml">
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101 <assert_contents>
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102 <is_valid_xml/>
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103 </assert_contents>
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104 </output>
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105 <assert_stdout>
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106 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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107 </assert_stdout>
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108 </test>
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109 <!-- TOPP_DatabaseFilter_3 -->
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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="DatabaseFilter_3.fasta"/>
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116 <param name="id" value="DatabaseFilter_3.mzid"/>
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117 <param name="method" value="whitelist"/>
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118 <output name="out" value="DatabaseFilter_3_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
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119 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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120 <output name="ctd_out" ftype="xml">
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121 <assert_contents>
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122 <is_valid_xml/>
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123 </assert_contents>
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124 </output>
15
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125 <assert_stdout>
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126 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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127 </assert_stdout>
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128 </test>
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129 <!-- TOPP_DatabaseFilter_4 -->
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130 <test expect_num_outputs="2">
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131 <section name="adv_opts">
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132 <param name="force" value="false"/>
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133 <param name="test" value="true"/>
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134 </section>
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135 <param name="in" value="DatabaseFilter_3.fasta"/>
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136 <param name="id" value="DatabaseFilter_3.mzid"/>
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137 <param name="method" value="blacklist"/>
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138 <output name="out" value="DatabaseFilter_4_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
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139 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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140 <output name="ctd_out" ftype="xml">
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141 <assert_contents>
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142 <is_valid_xml/>
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143 </assert_contents>
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144 </output>
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145 <assert_stdout>
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146 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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147 </assert_stdout>
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148 </test>
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149 </tests>
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150 <help><![CDATA[Filters a protein database (FASTA format) based on identified proteins
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151
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152
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153 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DatabaseFilter.html]]></help>
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154 <expand macro="references"/>
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155 </tool>