Mercurial > repos > galaxyp > openms_openswathfeaturexmltotsv

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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 21:29:01 +0000
parents 844c32358954
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3d7142328ec2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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: [Targeted Experiments and OpenSWATH]-->
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3 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Converts a featureXML to a mProphet tsv</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</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_cond.in &&
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17 #if $in_cond.in_select == "no"
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18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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20 #else
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21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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22 #end if
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23 mkdir tr &&
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24 cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
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25 mkdir out &&
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27 ## Main program call
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29 set -o pipefail &&
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30 @EXECUTABLE@ -write_ctd ./ &&
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31 python3 '$__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 -in
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34 #if $in_cond.in_select == "no"
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35 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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36 #else
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37 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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38 #end if
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39 -tr
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40 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
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41 -out
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42 'out/output.${gxy2omsext("csv")}'
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43
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44 ## Postprocessing
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45 && mv 'out/output.${gxy2omsext("csv")}' '$out'
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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 <conditional name="in_cond">
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55 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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56 <option value="no">No: process all datasets jointly</option>
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57 <option value="yes">Yes: process each dataset in an independent job</option>
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58 </param>
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59 <when value="no">
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60 <param argument="-in" type="data" format="featurexml" multiple="true" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
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61 </when>
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62 <when value="yes">
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63 <param argument="-in" type="data" format="featurexml" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
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64 </when>
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65 </conditional>
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66 <param argument="-tr" type="data" format="traml" label="TraML transition file" help=" select traml data sets(s)"/>
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67 <param argument="-short_format" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write short (one peptide per line) or long format (one transition per line)" help=""/>
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68 <param argument="-best_scoring_peptide" type="text" optional="true" value="" label="If only the best scoring feature per peptide should be printed, give the variable name" help="">
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69 <expand macro="list_string_san" name="best_scoring_peptide"/>
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70 </param>
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71 <expand macro="adv_opts_macro">
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72 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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73 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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74 <expand macro="list_string_san" name="test"/>
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75 </param>
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76 </expand>
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77 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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78 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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79 </param>
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80 </inputs>
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81 <outputs>
8
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82 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
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83 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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84 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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85 </data>
0
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86 </outputs>
13
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87 <tests>
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88 <!-- TOPP_OpenSwathFeatureXMLToTSV_test_1 -->
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89 <test expect_num_outputs="2">
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90 <section name="adv_opts">
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91 <param name="force" value="false"/>
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92 <param name="test" value="true"/>
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93 </section>
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94 <conditional name="in_cond">
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95 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
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96 </conditional>
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97 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
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98 <output name="out" value="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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99 <param name="short_format" value="true"/>
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100 <param name="best_scoring_peptide" value=""/>
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101 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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102 <output name="ctd_out" ftype="xml">
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103 <assert_contents>
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104 <is_valid_xml/>
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105 </assert_contents>
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106 </output>
13
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107 <assert_stdout>
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108 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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109 </assert_stdout>
12
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110 </test>
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111 <!-- TOPP_OpenSwathFeatureXMLToTSV_test_2 -->
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112 <test expect_num_outputs="2">
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113 <section name="adv_opts">
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114 <param name="force" value="false"/>
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115 <param name="test" value="true"/>
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116 </section>
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117 <conditional name="in_cond">
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118 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
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119 </conditional>
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120 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
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121 <output name="out" value="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
12
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122 <param name="short_format" value="false"/>
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123 <param name="best_scoring_peptide" value=""/>
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124 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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125 <output name="ctd_out" ftype="xml">
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126 <assert_contents>
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127 <is_valid_xml/>
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128 </assert_contents>
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129 </output>
13
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130 <assert_stdout>
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131 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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132 </assert_stdout>
12
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133 </test>
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134 <!-- TOPP_OpenSwathFeatureXMLToTSV_test_3 -->
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135 <test expect_num_outputs="2">
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136 <section name="adv_opts">
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137 <param name="force" value="false"/>
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138 <param name="test" value="true"/>
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139 </section>
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140 <conditional name="in_cond">
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141 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
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142 </conditional>
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143 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
13
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144 <output name="out" value="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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145 <param name="short_format" value="true"/>
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146 <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/>
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147 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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148 <output name="ctd_out" ftype="xml">
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149 <assert_contents>
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150 <is_valid_xml/>
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151 </assert_contents>
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152 </output>
13
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153 <assert_stdout>
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154 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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155 </assert_stdout>
12
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156 </test>
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157 </tests>
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158 <help><![CDATA[Converts a featureXML to a mProphet tsv.
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159
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160
13
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161 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathFeatureXMLToTSV.html]]></help>
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b8192a9b7f9c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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162 <expand macro="references"/>
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c1f46b63e8c8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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163 </tool>