Mercurial > repos > galaxyp > openms_databasefilter

annotate DatabaseFilter.xml @ 14:0878a55de9e7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:17:07 +0000
parents 0c98acedb17a
children 2f7a8b58314e
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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="DatabaseFilter" name="DatabaseFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Filters a protein database (FASTA format) based on identified proteins</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">DatabaseFilter</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 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 mkdir id &&
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20 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
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21 mkdir out &&
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23 ## Main program call
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24
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 -id
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32 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
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33 -out
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34 'out/output.${gxy2omsext("fasta")}'
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35
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36 ## Postprocessing
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37 && mv 'out/output.${gxy2omsext("fasta")}' '$out'
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38 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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39 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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40 #end if]]></command>
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41 <configfiles>
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42 <inputs name="args_json" data_style="paths"/>
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43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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44 </configfiles>
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45 <inputs>
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46 <param argument="-in" type="data" format="fasta" optional="false" label="Input FASTA file, containing a database" help=" select fasta data sets(s)"/>
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47 <param argument="-id" type="data" format="idxml,mzid" optional="false" label="Input file containing identified peptides and proteins" help=" select idxml,mzid data sets(s)"/>
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48 <param argument="-method" type="select" optional="true" label="Switch between white-/blacklisting" help="">
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49 <option value="whitelist" selected="true">whitelist</option>
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50 <option value="blacklist">blacklist</option>
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51 <expand macro="list_string_san" name="method"/>
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52 </param>
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53 <expand macro="adv_opts_macro">
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54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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55 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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56 <expand macro="list_string_san" name="test"/>
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57 </param>
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58 </expand>
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59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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61 </param>
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62 </inputs>
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63 <outputs>
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64 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/>
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65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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67 </data>
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68 </outputs>
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69 <tests><!-- UTILS_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" file="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 </test>
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86 <!-- UTILS_DatabaseFilter_2 -->
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87 <test expect_num_outputs="2">
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88 <section name="adv_opts">
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89 <param name="force" value="false"/>
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90 <param name="test" value="true"/>
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91 </section>
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92 <param name="in" value="DatabaseFilter_1.fasta"/>
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93 <param name="id" value="DatabaseFilter_1.idXML"/>
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94 <param name="method" value="blacklist"/>
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95 <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
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96 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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97 <output name="ctd_out" ftype="xml">
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98 <assert_contents>
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99 <is_valid_xml/>
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100 </assert_contents>
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101 </output>
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102 </test>
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103 <!-- UTILS_DatabaseFilter_3 -->
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104 <test expect_num_outputs="2">
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105 <section name="adv_opts">
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106 <param name="force" value="false"/>
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107 <param name="test" value="true"/>
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108 </section>
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109 <param name="in" value="DatabaseFilter_3.fasta"/>
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110 <param name="id" value="DatabaseFilter_3.mzid"/>
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111 <param name="method" value="whitelist"/>
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112 <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
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113 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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114 <output name="ctd_out" ftype="xml">
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115 <assert_contents>
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116 <is_valid_xml/>
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117 </assert_contents>
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118 </output>
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119 </test>
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120 <!-- UTILS_DatabaseFilter_4 -->
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121 <test expect_num_outputs="2">
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122 <section name="adv_opts">
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123 <param name="force" value="false"/>
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124 <param name="test" value="true"/>
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125 </section>
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126 <param name="in" value="DatabaseFilter_3.fasta"/>
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127 <param name="id" value="DatabaseFilter_3.mzid"/>
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128 <param name="method" value="blacklist"/>
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129 <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
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130 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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131 <output name="ctd_out" ftype="xml">
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132 <assert_contents>
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133 <is_valid_xml/>
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134 </assert_contents>
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135 </output>
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136 </test>
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137 </tests>
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138 <help><![CDATA[Filters a protein database (FASTA format) based on identified proteins
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139
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140
14
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141 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DatabaseFilter.html]]></help>
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142 <expand macro="references"/>
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143 </tool>