Mercurial > repos > galaxyp > openms_fileinfo
diff 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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--- a/FileInfo.xml Thu Dec 01 19:16:37 2022 +0000 +++ b/FileInfo.xml Fri Jun 14 21:32:58 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 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> + <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> @@ -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($in.ext)' && mkdir out && #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_tsv && @@ -52,7 +51,7 @@ <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" optional="false" 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="-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=""/> @@ -62,7 +61,7 @@ <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" 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> @@ -80,14 +79,15 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_FileInfo_1 --> + <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" file="FileInfo_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -101,6 +101,9 @@ <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_FileInfo_2 --> <test expect_num_outputs="2"> @@ -109,7 +112,7 @@ <param name="test" value="true"/> </section> <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/> - <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -123,6 +126,9 @@ <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_FileInfo_3 --> <test expect_num_outputs="2"> @@ -131,7 +137,7 @@ <param name="test" value="true"/> </section> <param name="in" value="FileInfo_3_input.featureXML"/> - <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -145,6 +151,9 @@ <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_FileInfo_4 --> <test expect_num_outputs="2"> @@ -153,7 +162,7 @@ <param name="test" value="true"/> </section> <param name="in" value="FileInfo_4_input.mzXML"/> - <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -167,6 +176,9 @@ <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_FileInfo_5 --> <test expect_num_outputs="2"> @@ -175,7 +187,7 @@ <param name="test" value="true"/> </section> <param name="in" value="FileInfo_5_input.mzDat"/> - <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -189,6 +201,9 @@ <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_FileInfo_6 --> <test expect_num_outputs="2"> @@ -197,7 +212,7 @@ <param name="test" value="true"/> </section> <param name="in" value="FileInfo_6_input.mzData"/> - <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -211,6 +226,9 @@ <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_FileInfo_7 --> <test expect_num_outputs="2"> @@ -219,7 +237,7 @@ <param name="test" value="true"/> </section> <param name="in" value="FileInfo_7_input.consensusXML"/> - <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -233,6 +251,9 @@ <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_FileInfo_9 --> <test expect_num_outputs="2"> @@ -241,7 +262,7 @@ <param name="test" value="true"/> </section> <param name="in" value="FileInfo_9_input.mzML"/> - <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -255,6 +276,9 @@ <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_FileInfo_10 --> <test expect_num_outputs="2"> @@ -263,7 +287,7 @@ <param name="test" value="true"/> </section> <param name="in" value="FileInfo_10_input.idXML"/> - <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -277,6 +301,9 @@ <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_FileInfo_12 --> <test expect_num_outputs="2"> @@ -298,6 +325,9 @@ <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_FileInfo_13 --> <test expect_num_outputs="2"> @@ -319,6 +349,9 @@ <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_FileInfo_14 --> <test expect_num_outputs="2"> @@ -327,7 +360,7 @@ <param name="test" value="true"/> </section> <param name="in" value="FileInfo_14_input.mzid"/> - <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -341,6 +374,9 @@ <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_FileInfo_15 --> <test expect_num_outputs="2"> @@ -349,7 +385,7 @@ <param name="test" value="true"/> </section> <param name="in" value="FileInfo_15_input.mzid"/> - <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -363,6 +399,9 @@ <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_FileInfo_16 --> <test expect_num_outputs="2"> @@ -371,7 +410,32 @@ <param name="test" value="true"/> </section> <param name="in" value="FileInfo_16_input.trafoXML"/> - <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -385,15 +449,18 @@ <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 --> + <!-- 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_17_input.fasta"/> - <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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"/> @@ -407,19 +474,22 @@ <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 --> + <!-- 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="FileInfo_18_input.fasta"/> - <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <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="false"/> + <param name="d" value="true"/> <param name="c" value="false"/> <param name="v" value="false"/> <param name="i" value="false"/> @@ -429,11 +499,14 @@ <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[Shows basic information about the file, such as data ranges and file type. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileInfo.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileInfo.html]]></help> <expand macro="references"/> </tool>