Mercurial > repos > galaxyp > openms_openswathfeaturexmltotsv

annotate OpenSwathFeatureXMLToTSV.xml @ 12:844c32358954 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 19:21:34 +0000
parents 5c50095229a5
children 604c9363dcfd
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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: [Targeted Experiments]-->
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4 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Converts a featureXML to a mProphet tsv.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</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_cond.in &&
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18 #if $in_cond.in_select == "no"
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19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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20 ${' '.join(["ln -s '%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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21 #else
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22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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23 #end if
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24 mkdir tr &&
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25 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
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26 mkdir out &&
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28 ## Main program call
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30 set -o pipefail &&
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31 @EXECUTABLE@ -write_ctd ./ &&
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32 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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33 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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34 -in
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35 #if $in_cond.in_select == "no"
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36 ${' '.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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37 #else
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38 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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39 #end if
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40 -tr
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41 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
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42 -out
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43 'out/output.${gxy2omsext("csv")}'
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44
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45 ## Postprocessing
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46 && mv 'out/output.${gxy2omsext("csv")}' '$out'
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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 <conditional name="in_cond">
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56 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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57 <option value="no">No: process all datasets jointly</option>
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58 <option value="yes">Yes: process each dataset in an independent job</option>
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59 </param>
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60 <when value="no">
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61 <param argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
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62 </when>
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63 <when value="yes">
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64 <param argument="-in" type="data" format="featurexml" multiple="false" optional="false" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
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65 </when>
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66 </conditional>
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67 <param argument="-tr" type="data" format="traml" optional="false" label="TraML transition file" help=" select traml data sets(s)"/>
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68 <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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69 <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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70 <expand macro="list_string_san" name="best_scoring_peptide"/>
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71 </param>
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72 <expand macro="adv_opts_macro">
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73 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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74 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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75 <expand macro="list_string_san" name="test"/>
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76 </param>
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77 </expand>
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78 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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79 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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80 </param>
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81 </inputs>
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82 <outputs>
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83 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
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84 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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85 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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86 </data>
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87 </outputs>
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88 <tests><!-- 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" file="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>
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107 </test>
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108 <!-- TOPP_OpenSwathFeatureXMLToTSV_test_2 -->
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109 <test expect_num_outputs="2">
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110 <section name="adv_opts">
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111 <param name="force" value="false"/>
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112 <param name="test" value="true"/>
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113 </section>
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114 <conditional name="in_cond">
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115 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
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116 </conditional>
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117 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
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118 <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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119 <param name="short_format" value="false"/>
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120 <param name="best_scoring_peptide" value=""/>
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121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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122 <output name="ctd_out" ftype="xml">
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123 <assert_contents>
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124 <is_valid_xml/>
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125 </assert_contents>
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126 </output>
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127 </test>
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128 <!-- TOPP_OpenSwathFeatureXMLToTSV_test_3 -->
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129 <test expect_num_outputs="2">
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130 <section name="adv_opts">
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131 <param name="force" value="false"/>
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132 <param name="test" value="true"/>
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133 </section>
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134 <conditional name="in_cond">
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135 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
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136 </conditional>
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137 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
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138 <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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139 <param name="short_format" value="true"/>
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140 <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/>
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141 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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142 <output name="ctd_out" ftype="xml">
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143 <assert_contents>
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144 <is_valid_xml/>
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145 </assert_contents>
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146 </output>
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147 </test>
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148 </tests>
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149 <help><![CDATA[Converts a featureXML to a mProphet tsv.
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150
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151
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152 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathFeatureXMLToTSV.html]]></help>
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153 <expand macro="references"/>
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154 </tool>