Mercurial > repos > galaxyp > openms_masscalculator
diff MassCalculator.xml @ 14:d905af02ce63 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 21:36:45 +0000 |
| parents | bcd50cd4fe42 |
| children |
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--- a/MassCalculator.xml Thu Dec 01 19:08:33 2022 +0000 +++ b/MassCalculator.xml Fri Jun 14 21:36:45 2024 +0000 @@ -1,6 +1,5 @@ -<?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: [Utilities]--> +<!--Proposed Tool Section: [Misc / Helpers]--> <tool id="MassCalculator" name="MassCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Calculates masses and mass-to-charge ratios of peptide sequences</description> <macros> @@ -16,7 +15,7 @@ ## Preprocessing #if $in: mkdir in && - ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && + cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && @@ -57,10 +56,10 @@ <expand macro="list_string_val" name="in_seq"/> <expand macro="list_string_san" name="in_seq"/> </param> - <param argument="-charge" type="text" optional="true" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param argument="-charge" type="text" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_integer_valsan" name="charge"/> </param> - <param argument="-format" type="select" optional="true" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help=""> + <param argument="-format" type="select" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help=""> <option value="list" selected="true">list</option> <option value="table">table</option> <option value="mass_only">mass_only</option> @@ -68,7 +67,7 @@ <expand macro="list_string_san" name="format"/> </param> <param argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) peptide masses" help=""/> - <param argument="-fragment_type" type="select" optional="true" label="For what type of sequence/fragment the mass should be computed" help=""> + <param argument="-fragment_type" type="select" label="For what type of sequence/fragment the mass should be computed" help=""> <option value="full" selected="true">full</option> <option value="internal">internal</option> <option value="N-terminal">N-terminal</option> @@ -86,7 +85,7 @@ </param> <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> @@ -106,15 +105,15 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- UTILS_MassCalculator_1 --> + <tests> + <!-- TOPP_MassCalculator_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="MassCalculator_1_input.tsv" ftype="tabular"/> - <param name="in_seq" value=""/> - <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="out" value="MassCalculator_1_output.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> <param name="charge" value="0 1"/> <param name="format" value="table"/> <param name="average_mass" value="false"/> @@ -126,15 +125,18 @@ <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> - <!-- UTILS_MassCalculator_2 --> + <!-- TOPP_MassCalculator_2 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in_seq" value=""LDQWLC(Carbamidomethyl)EKL" "(Glu->pyro-Glu)EAM(Oxidation)APKHK" "RANVM(Oxidation)DYR" "FGVEQDVDMVFASFIR""/> - <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="out" value="MassCalculator_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> <param name="charge" value="1 2 3"/> <param name="format" value="list"/> <param name="average_mass" value="false"/> @@ -146,11 +148,14 @@ <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[Calculates masses and mass-to-charge ratios of peptide sequences -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MassCalculator.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MassCalculator.html]]></help> <expand macro="references"/> </tool>