Mercurial > repos > galaxyp > openms_masscalculator
diff MassCalculator.xml @ 13:bcd50cd4fe42 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:08:33 +0000 |
| parents | 65c6e741ddf3 |
| children | d905af02ce63 |
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--- a/MassCalculator.xml Fri Nov 06 20:21:38 2020 +0000 +++ b/MassCalculator.xml Thu Dec 01 19:08:33 2022 +0000 @@ -1,13 +1,11 @@ <?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]--> -<tool id="MassCalculator" name="MassCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<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> <token name="@EXECUTABLE@">MassCalculator</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -54,23 +52,23 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="tabular" optional="true" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select tabular data sets(s)"/> - <param name="in_seq" argument="-in_seq" type="text" optional="true" value="" label="List of peptide sequences (mutually exclusive to 'in')" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <param argument="-in" type="data" format="tabular" optional="true" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select tabular data sets(s)"/> + <param argument="-in_seq" type="text" optional="true" value="" label="List of peptide sequences (mutually exclusive to 'in')" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="in_seq"/> + <expand macro="list_string_san" name="in_seq"/> </param> - <param name="charge" 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)"> - <expand macro="list_integer_valsan"/> + <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)"> + <expand macro="list_integer_valsan" name="charge"/> </param> - <param name="format" argument="-format" display="radio" type="select" optional="false" 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" 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=""> <option value="list" selected="true">list</option> <option value="table">table</option> <option value="mass_only">mass_only</option> <option value="mz_only">mz_only</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="format"/> </param> - <param name="average_mass" argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) peptide masses" help=""/> - <param name="fragment_type" argument="-fragment_type" type="select" optional="false" label="For what type of sequence/fragment the mass should be computed" help=""> + <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=""> <option value="full" selected="true">full</option> <option value="internal">internal</option> <option value="N-terminal">N-terminal</option> @@ -81,15 +79,15 @@ <option value="x-ion">x-ion</option> <option value="y-ion">y-ion</option> <option value="z-ion">z-ion</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="fragment_type"/> </param> - <param name="separator" argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help=""> - <expand macro="list_string_san"/> + <param argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help=""> + <expand macro="list_string_san" name="separator"/> </param> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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 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=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -108,13 +106,51 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_MassCalculator"/> - <expand macro="manutest_MassCalculator"/> + <tests><!-- UTILS_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"/> + <param name="charge" value="0 1"/> + <param name="format" value="table"/> + <param name="average_mass" value="false"/> + <param name="fragment_type" value="full"/> + <param name="separator" value=","/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- UTILS_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"/> + <param name="charge" value="1 2 3"/> + <param name="format" value="list"/> + <param name="average_mass" value="false"/> + <param name="fragment_type" value="full"/> + <param name="separator" value=""/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MassCalculator.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MassCalculator.html]]></help> <expand macro="references"/> </tool>