Mercurial > repos > galaxyp > openms_textexporter
diff TextExporter.xml @ 14:b5de4c3efbdd draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:44:36 +0000 |
| parents | 1b03536aa3c9 |
| children |
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--- a/TextExporter.xml Thu Dec 01 19:08:22 2022 +0000 +++ b/TextExporter.xml Fri Jun 14 21:44:36 2024 +0000 @@ -1,8 +1,7 @@ -<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> -<!--Proposed Tool Section: [File Handling]--> +<!--Proposed Tool Section: [File Converter]--> <tool id="TextExporter" name="TextExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Exports various XML formats to a text file.</description> + <description>Exports various XML formats to a text file</description> <macros> <token name="@EXECUTABLE@">TextExporter</token> <import>macros.xml</import> @@ -15,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir consensus_centroids && @@ -72,17 +71,18 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/> - <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension, ambiguous file extensions are interpreted as tsv" help=""> + <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" label="Input file" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/> + <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension, ambiguous file extensions are interpreted as tsv" help=""> <option value="csv">csv</option> <option value="tsv">tabular (tsv)</option> <option value="txt">txt</option> + <validator type="expression" message="A value needs to be selected">value != "select a value"</validator> <expand macro="list_string_san" name="out_type"/> </param> - <param argument="-replacement" type="text" optional="true" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help=""> + <param argument="-replacement" type="text" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help=""> <expand macro="list_string_san" name="replacement"/> </param> - <param argument="-quoting" type="select" optional="true" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes"> + <param argument="-quoting" type="select" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes"> <option value="none" selected="true">none</option> <option value="double">double</option> <option value="escape">escape</option> @@ -91,19 +91,19 @@ <param argument="-no_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppresses output of identification data" help=""/> <section name="feature" title="Options for featureXML input files" help="" expanded="false"> <param name="minimal" argument="-feature:minimal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to write only three attributes: RT, m/z, and intensity" help=""/> - <param name="add_metavalues" argument="-feature:add_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> + <param name="add_metavalues" argument="-feature:add_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> </section> <section name="id" title="Options for idXML input files" help="" expanded="false"> <param name="proteins_only" argument="-id:proteins_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only protein information from an idXML file" help=""/> <param name="peptides_only" argument="-id:peptides_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only peptide information from an idXML file" help=""/> <param name="protein_groups" argument="-id:protein_groups" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want to also write indist" help="group information from an idXML file"/> <param name="first_dim_rt" argument="-id:first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" help=""/> - <param name="add_metavalues" argument="-id:add_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideID (=spectrum) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> - <param name="add_hit_metavalues" argument="-id:add_hit_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideHit (=PSM) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> - <param name="add_protein_hit_metavalues" argument="-id:add_protein_hit_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values on protein level which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> + <param name="add_metavalues" argument="-id:add_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideID (=spectrum) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> + <param name="add_hit_metavalues" argument="-id:add_hit_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideHit (=PSM) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> + <param name="add_protein_hit_metavalues" argument="-id:add_protein_hit_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values on protein level which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> </section> <section name="consensus" title="Options for consensusXML input files" help="" expanded="false"> - <param name="sorting_method" argument="-consensus:sorting_method" type="select" optional="true" label="Sorting options can be combined" help="The precedence is: sort_by_size, sort_by_maps, sorting_method"> + <param name="sorting_method" argument="-consensus:sorting_method" type="select" label="Sorting options can be combined" help="The precedence is: sort_by_size, sort_by_maps, sorting_method"> <option value="none" selected="true">none</option> <option value="RT">RT</option> <option value="MZ">MZ</option> @@ -115,10 +115,11 @@ </param> <param name="sort_by_maps" argument="-consensus:sort_by_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by the covered maps, lexicographically" help=""/> <param name="sort_by_size" argument="-consensus:sort_by_size" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by decreasing size" help="(i.e., the number of elements)"/> + <param name="add_metavalues" argument="-consensus:add_metavalues" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add columns for ConsensusFeature meta values" help=""/> </section> <expand macro="adv_opts_macro"> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -149,14 +150,15 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_TextExporter_1 --> + <tests> + <!-- TOPP_TextExporter_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="TextExporter_1_input.featureXML"/> - <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <output name="out" value="TextExporter_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="out_type" value="txt"/> <param name="replacement" value="_"/> <param name="quoting" value="none"/> @@ -178,6 +180,7 @@ <param name="sorting_method" value="none"/> <param name="sort_by_maps" value="false"/> <param name="sort_by_size" value="false"/> + <param name="add_metavalues" value="false"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -185,6 +188,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_TextExporter_2 --> <test expect_num_outputs="5"> @@ -193,7 +199,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TextExporter_2_input.consensusXML"/> - <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <output name="out" value="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/> <param name="out_type" value="tsv"/> <param name="replacement" value="_"/> <param name="quoting" value="none"/> @@ -215,16 +221,20 @@ <param name="sorting_method" value="RT_then_MZ"/> <param name="sort_by_maps" value="true"/> <param name="sort_by_size" value="true"/> + <param name="add_metavalues" value="true"/> </section> - <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="consensus_centroids" value="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="consensus_elements" value="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="consensus_features" value="TextExporter_2_consensus_features.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_TextExporter_3 --> <test expect_num_outputs="2"> @@ -233,7 +243,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TextExporter_3_input.idXML"/> - <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <output name="out" value="TextExporter_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="out_type" value="txt"/> <param name="replacement" value="_"/> <param name="quoting" value="none"/> @@ -255,6 +265,7 @@ <param name="sorting_method" value="none"/> <param name="sort_by_maps" value="false"/> <param name="sort_by_size" value="false"/> + <param name="add_metavalues" value="false"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -262,6 +273,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_TextExporter_4 --> <test expect_num_outputs="2"> @@ -270,7 +284,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TextExporter_3_input.idXML"/> - <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <output name="out" value="TextExporter_4_output_proteins.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="out_type" value="txt"/> <param name="replacement" value="_"/> <param name="quoting" value="none"/> @@ -292,6 +306,7 @@ <param name="sorting_method" value="none"/> <param name="sort_by_maps" value="false"/> <param name="sort_by_size" value="false"/> + <param name="add_metavalues" value="false"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -299,6 +314,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_TextExporter_5 --> <test expect_num_outputs="2"> @@ -307,7 +325,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TextExporter_5_input.idXML"/> - <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <output name="out" value="TextExporter_5_output_peptides.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="out_type" value="txt"/> <param name="replacement" value="_"/> <param name="quoting" value="none"/> @@ -329,6 +347,7 @@ <param name="sorting_method" value="none"/> <param name="sort_by_maps" value="false"/> <param name="sort_by_size" value="false"/> + <param name="add_metavalues" value="false"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -336,6 +355,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_TextExporter_6 --> <test expect_num_outputs="2"> @@ -344,7 +366,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TextExporter_6_input.featureXML"/> - <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <output name="out" value="TextExporter_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="out_type" value="txt"/> <param name="replacement" value="_"/> <param name="quoting" value="none"/> @@ -366,6 +388,7 @@ <param name="sorting_method" value="none"/> <param name="sort_by_maps" value="false"/> <param name="sort_by_size" value="false"/> + <param name="add_metavalues" value="false"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -373,6 +396,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_TextExporter_7 --> <test expect_num_outputs="2"> @@ -381,7 +407,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TextExporter_7_input.consensusXML"/> - <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <output name="out" value="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/> <param name="out_type" value="tsv"/> <param name="replacement" value="_"/> <param name="quoting" value="none"/> @@ -403,6 +429,7 @@ <param name="sorting_method" value="RT_then_MZ"/> <param name="sort_by_maps" value="true"/> <param name="sort_by_size" value="true"/> + <param name="add_metavalues" value="false"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -410,6 +437,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_TextExporter_8 --> <test expect_num_outputs="2"> @@ -418,7 +448,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TextExporter_1_input.featureXML"/> - <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <output name="out" value="TextExporter_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="out_type" value="txt"/> <param name="replacement" value="_"/> <param name="quoting" value="none"/> @@ -440,6 +470,7 @@ <param name="sorting_method" value="none"/> <param name="sort_by_maps" value="false"/> <param name="sort_by_size" value="false"/> + <param name="add_metavalues" value="false"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -447,6 +478,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_TextExporter_9 --> <test expect_num_outputs="2"> @@ -455,7 +489,7 @@ <param name="test" value="true"/> </section> <param name="in" value="TextExporter_9_input.idXML"/> - <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <output name="out" value="TextExporter_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="out_type" value="txt"/> <param name="replacement" value="_"/> <param name="quoting" value="none"/> @@ -477,6 +511,7 @@ <param name="sorting_method" value="none"/> <param name="sort_by_maps" value="false"/> <param name="sort_by_size" value="false"/> + <param name="add_metavalues" value="false"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> @@ -484,11 +519,14 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> </tests> <help><![CDATA[Exports various XML formats to a text file. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_TextExporter.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TextExporter.html]]></help> <expand macro="references"/> </tool>