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view FileInfo.xml @ 16:5a45e6ac9aae 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 21:32:58 +0000 |
| parents | 4af67edd5aef |
| children |
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<!--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 Filtering / Extraction / Merging]--> <tool id="FileInfo" name="FileInfo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Shows basic information about the file, such as data ranges and file type</description> <macros> <token name="@EXECUTABLE@">FileInfo</token> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ @EXT_FOO@ #import re ## Preprocessing mkdir in && cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_tsv && #end if ## 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($in.ext)' -out 'out/output.${gxy2omsext("txt")}' #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out_tsv 'out_tsv/output.${gxy2omsext("csv")}' #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if ## Postprocessing && mv 'out/output.${gxy2omsext("txt")}' '$out' #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out_tsv/output.${gxy2omsext("csv")}' '$out_tsv' #end if #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 argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml data sets(s)"/> <param argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/> <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/> <param argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/> <param argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/> <param argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/> <param argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/> <param argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/> <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" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> <option value="out_tsv_FLAG">out_tsv (Second optional output file)</option> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> <outputs> <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/> <data name="out_tsv" label="${tool.name} on ${on_string}: out_tsv" format="csv"> <filter>OPTIONAL_OUTPUTS is not None and "out_tsv_FLAG" in OPTIONAL_OUTPUTS</filter> </data> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> <tests> <!-- TOPP_FileInfo_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="FileInfo_1_input.dta" ftype="dta"/> <output name="out" value="FileInfo_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="false"/> <param name="p" value="false"/> <param name="s" value="false"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_2 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/> <output name="out" value="FileInfo_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="false"/> <param name="p" value="false"/> <param name="s" value="false"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_3 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_3_input.featureXML"/> <output name="out" value="FileInfo_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="true"/> <param name="p" value="true"/> <param name="s" value="true"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_4 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_4_input.mzXML"/> <output name="out" value="FileInfo_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="true"/> <param name="p" value="false"/> <param name="s" value="false"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_5 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_5_input.mzDat"/> <output name="out" value="FileInfo_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="true"/> <param name="p" value="false"/> <param name="s" value="true"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_6 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_6_input.mzData"/> <output name="out" value="FileInfo_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="false"/> <param name="p" value="false"/> <param name="s" value="true"/> <param name="d" value="true"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_7 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_7_input.consensusXML"/> <output name="out" value="FileInfo_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="true"/> <param name="p" value="true"/> <param name="s" value="true"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_9 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_9_input.mzML"/> <output name="out" value="FileInfo_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="true"/> <param name="p" value="true"/> <param name="s" value="true"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_10 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_10_input.idXML"/> <output name="out" value="FileInfo_10_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="false"/> <param name="p" value="false"/> <param name="s" value="false"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_12 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_12_input.mzML"/> <param name="m" value="false"/> <param name="p" value="false"/> <param name="s" value="false"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="true"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_13 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_13_input.consensusXML"/> <param name="m" value="false"/> <param name="p" value="false"/> <param name="s" value="false"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_14 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_14_input.mzid"/> <output name="out" value="FileInfo_14_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="false"/> <param name="p" value="false"/> <param name="s" value="false"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="true"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_15 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_15_input.mzid"/> <output name="out" value="FileInfo_15_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="false"/> <param name="p" value="false"/> <param name="s" value="false"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="true"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_16 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_16_input.trafoXML"/> <output name="out" value="FileInfo_16_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="false"/> <param name="p" value="false"/> <param name="s" value="false"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_17 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_17_input.fasta"/> <output name="out" value="FileInfo_17_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="false"/> <param name="p" value="false"/> <param name="s" value="false"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_18 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FileInfo_18_input.fasta"/> <output name="out" value="FileInfo_18_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="false"/> <param name="p" value="false"/> <param name="s" value="false"/> <param name="d" value="false"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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_FileInfo_19 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FAIMS_test_data.mzML"/> <output name="out" value="FileInfo_19_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="m" value="false"/> <param name="p" value="false"/> <param name="s" value="false"/> <param name="d" value="true"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_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> </tests> <help><![CDATA[Shows basic information about the file, such as data ranges and file type. For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileInfo.html]]></help> <expand macro="references"/> </tool>