Mercurial > repos > galaxyp > openms_textexporter
diff TextExporter.xml @ 9:27aeff17fd2e draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
| author | galaxyp |
|---|---|
| date | Thu, 27 Aug 2020 19:45:29 -0400 |
| parents | 3a2a31d4032c |
| children | 1c596fdaf34a |
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--- a/TextExporter.xml Fri May 17 09:57:49 2019 -0400 +++ b/TextExporter.xml Thu Aug 27 19:45:29 2020 -0400 @@ -1,144 +1,167 @@ <?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]--> -<tool id="TextExporter" name="TextExporter" version="2.3.0"> +<tool id="TextExporter" name="TextExporter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Exports various XML formats to a text file.</description> <macros> <token name="@EXECUTABLE@">TextExporter</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> - <expand macro="stdio"/> <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[TextExporter + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $param_in: - -in $param_in +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir out && #end if -#if $param_out: - -out $param_out -#end if -#if $param_separator: - -separator "$param_separator" -#end if -#if $param_replacement: - -replacement "$param_replacement" +#if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir consensus_centroids && #end if -#if $param_quoting: - -quoting - #if " " in str($param_quoting): - "$param_quoting" - #else - $param_quoting - #end if +#if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir consensus_elements && #end if -#if $param_no_ids: - -no_ids -#end if -#if $param_feature_minimal: - -feature:minimal +#if "features_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir consensus_features && #end if -#if $param_feature_add_metavalues: - -feature:add_metavalues $param_feature_add_metavalues -#end if -#if $param_id_proteins_only: - -id:proteins_only + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -out + 'out/output.${gxy2omsext("csv")}' #end if -#if $param_id_peptides_only: - -id:peptides_only -#end if -#if $param_id_first_dim_rt: - -id:first_dim_rt -#end if -#if $param_id_add_metavalues: - -id:add_metavalues $param_id_add_metavalues +#if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -consensus:centroids + 'consensus_centroids/output.${gxy2omsext("csv")}' #end if -#if $param_id_add_hit_metavalues: - -id:add_hit_metavalues $param_id_add_hit_metavalues -#end if -#if $param_consensus_centroids: - -consensus:centroids $param_consensus_centroids +#if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -consensus:elements + 'consensus_elements/output.${gxy2omsext("csv")}' #end if -#if $param_consensus_elements: - -consensus:elements $param_consensus_elements -#end if -#if $param_consensus_features: - -consensus:features $param_consensus_features +#if "features_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -consensus:features + 'consensus_features/output.${gxy2omsext("csv")}' #end if -#if $param_consensus_sorting_method: - -consensus:sorting_method - #if " " in str($param_consensus_sorting_method): - "$param_consensus_sorting_method" - #else - $param_consensus_sorting_method - #end if +#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 + | tee '$stdout' #end if -#if $param_consensus_sort_by_maps: - -consensus:sort_by_maps + +## Postprocessing +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'out/output.${gxy2omsext("csv")}' '$out' #end if -#if $param_consensus_sort_by_size: - -consensus:sort_by_size +#if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'consensus_centroids/output.${gxy2omsext("csv")}' '$consensus_centroids' #end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force +#if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'consensus_elements/output.${gxy2omsext("csv")}' '$consensus_elements' +#end if +#if "features_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'consensus_features/output.${gxy2omsext("csv")}' '$consensus_features' #end if -#end if -]]></command> +#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS + && mv '@EXECUTABLE@.ctd' '$ctd_out' +#end if]]></command> + <configfiles> + <inputs name="args_json" data_style="paths"/> + <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <param name="param_in" type="data" format="featurexml,consensusxml,idxml,mzml" optional="False" label="Input file" help="(-in) "/> - <param name="param_separator" type="text" size="30" label="The used separator character(s); if not set the 'tab' character is used" help="(-separator) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/> + <param name="separator" argument="-separator" type="text" optional="true" value="" label="The used separator character(s); if not set the 'tab' character is used" help=""> + <expand macro="list_string_san"/> </param> - <param name="param_replacement" type="text" size="30" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="(-replacement) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="replacement" argument="-replacement" type="text" optional="true" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help=""> + <expand macro="list_string_san"/> </param> - <param name="param_quoting" display="radio" type="select" optional="False" value="none" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, <br>'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting) "> + <param name="quoting" argument="-quoting" display="radio" type="select" optional="false" 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> + <expand macro="list_string_san"/> </param> - <param name="param_no_ids" display="radio" type="boolean" truevalue="-no_ids" falsevalue="" checked="false" optional="True" label="Suppresses output of identification data" help="(-no_ids) "/> - <param name="param_feature_minimal" display="radio" type="boolean" truevalue="-feature:minimal" falsevalue="" checked="false" optional="True" label="Set this flag to write only three attributes: RT, m/z, and intensity" help="(-minimal) "/> - <param name="param_feature_add_metavalues" type="integer" min="-1" max="100" optional="True" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="(-add_metavalues) Set to -1 to omit meta values (default)"/> - <param name="param_id_proteins_only" display="radio" type="boolean" truevalue="-id:proteins_only" falsevalue="" checked="false" optional="True" label="Set this flag if you want only protein information from an idXML file" help="(-proteins_only) "/> - <param name="param_id_peptides_only" display="radio" type="boolean" truevalue="-id:peptides_only" falsevalue="" checked="false" optional="True" label="Set this flag if you want only peptide information from an idXML file" help="(-peptides_only) "/> - <param name="param_id_first_dim_rt" display="radio" type="boolean" truevalue="-id:first_dim_rt" falsevalue="" checked="false" optional="True" label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" help="(-first_dim_rt) "/> - <param name="param_id_add_metavalues" type="integer" min="-1" max="100" optional="True" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="(-add_metavalues) Set to -1 to omit meta values (default)"/> - <param name="param_id_add_hit_metavalues" type="integer" min="-1" max="100" optional="True" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="(-add_hit_metavalues) Set to -1 to omit meta values (default)"/> - <param name="param_consensus_sorting_method" type="select" optional="False" value="none" label="Sorting options can be combined" help="(-sorting_method) 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> - <option value="RT_then_MZ">RT_then_MZ</option> - <option value="intensity">intensity</option> - <option value="quality_decreasing">quality_decreasing</option> - <option value="quality_increasing">quality_increasing</option> + <param name="no_ids" 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)"/> + </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)"/> + </section> + <section name="consensus" title="Options for consensusXML input files" help="" expanded="false"> + <param name="sorting_method" argument="-consensus:sorting_method" type="select" optional="false" 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> + <option value="RT_then_MZ">RT_then_MZ</option> + <option value="intensity">intensity</option> + <option value="quality_decreasing">quality_decreasing</option> + <option value="quality_increasing">quality_increasing</option> + <expand macro="list_string_san"/> + </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)"/> + </section> + <expand macro="adv_opts_macro"> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> + </param> + </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> + <option value="out_FLAG">out (Apply a stable sort by decreasing size)</option> + <option value="centroids_FLAG">centroids (Apply a stable sort by decreasing size)</option> + <option value="elements_FLAG">elements (Apply a stable sort by decreasing size)</option> + <option value="features_FLAG">features (Apply a stable sort by decreasing size)</option> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> - <param name="param_consensus_sort_by_maps" display="radio" type="boolean" truevalue="-consensus:sort_by_maps" falsevalue="" checked="false" optional="True" label="Apply a stable sort by the covered maps, lexicographically" help="(-sort_by_maps) "/> - <param name="param_consensus_sort_by_size" display="radio" type="boolean" truevalue="-consensus:sort_by_size" falsevalue="" checked="false" optional="True" label="Apply a stable sort by decreasing size (i.e., the number of elements)" help="(-sort_by_size) "/> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> - </expand> </inputs> <outputs> - <data name="param_out" format="tabular"/> - <data name="param_consensus_centroids" format="tabular"/> - <data name="param_consensus_elements" format="tabular"/> - <data name="param_consensus_features" format="tabular"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="csv"> + <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="consensus_centroids" label="${tool.name} on ${on_string}: consensus:centroids" format="csv"> + <filter>OPTIONAL_OUTPUTS is not None and "centroids_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="consensus_elements" label="${tool.name} on ${on_string}: consensus:elements" format="csv"> + <filter>OPTIONAL_OUTPUTS is not None and "elements_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="consensus_features" label="${tool.name} on ${on_string}: consensus:features" format="csv"> + <filter>OPTIONAL_OUTPUTS is not None and "features_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> + <filter>OPTIONAL_OUTPUTS is None</filter> + </data> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Exports various XML formats to a text file. + <tests> + <expand macro="autotest_TextExporter"/> + <expand macro="manutest_TextExporter"/> + </tests> + <help><![CDATA[Exports various XML formats to a text file. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_TextExporter.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_TextExporter.html]]></help> + <expand macro="references"/> </tool>