Mercurial > repos > galaxyp > openms_mascotadapter
diff MascotAdapter.xml @ 13:27e308170367 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:12:19 +0000 |
| parents | 57fb2083a8cb |
| children | 087b9d721a08 |
line wrap: on
line diff
--- a/MascotAdapter.xml Fri Nov 06 20:12:23 2020 +0000 +++ b/MascotAdapter.xml Thu Dec 01 19:12:19 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: [Identification]--> -<tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Annotates MS/MS spectra using Mascot.</description> <macros> <token name="@EXECUTABLE@">MascotAdapter</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,18 +39,18 @@ <configfile name="hardcoded_json"><![CDATA[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mascotxml,mzdata" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/> - <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="output file type (for TOPPAS)" help=""> + <param argument="-in" type="data" format="mascotxml,mzdata" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/> + <param argument="-out_type" display="radio" type="select" optional="false" label="output file type (for TOPPAS)" help=""> <option value="idXML">idxml</option> <option value="mgf">mgf</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="out_type"/> </param> - <param name="instrument" argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help=""> - <expand macro="list_string_san"/> + <param argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help=""> + <expand macro="list_string_san" name="instrument"/> </param> - <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="2.0" label="the precursor mass tolerance" help=""/> - <param name="peak_mass_tolerance" argument="-peak_mass_tolerance" type="float" optional="true" value="1.0" label="the peak mass tolerance" help=""/> - <param name="taxonomy" argument="-taxonomy" type="select" optional="false" label="the taxonomy" help=""> + <param argument="-precursor_mass_tolerance" type="float" optional="true" value="2.0" label="the precursor mass tolerance" help=""/> + <param argument="-peak_mass_tolerance" type="float" optional="true" value="1.0" label="the peak mass tolerance" help=""/> + <param argument="-taxonomy" type="select" optional="true" label="the taxonomy" help=""> <option value="All entries" selected="true">All entries</option> <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option> <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option> @@ -118,27 +116,27 @@ <option value=". . Other (includes plasmids and artificial sequences)">. . Other (includes plasmids and artificial sequences)</option> <option value=". . unclassified">. . unclassified</option> <option value=". . Species information unavailable">. . Species information unavailable</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="taxonomy"/> </param> - <param name="modifications" argument="-modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" 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="-modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="modifications"/> + <expand macro="list_string_san" name="modifications"/> </param> - <param name="variable_modifications" argument="-variable_modifications" type="text" optional="true" value="" label="the variable modifications i.e. Carboxymethyl (C)" 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="-variable_modifications" type="text" optional="true" value="" label="the variable modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="variable_modifications"/> + <expand macro="list_string_san" name="variable_modifications"/> </param> - <param name="charges" argument="-charges" type="text" optional="true" value="1+ 2+ 3+" label="the different charge states" 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="-charges" type="text" optional="true" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="charges"/> + <expand macro="list_string_san" name="charges"/> </param> - <param name="db" argument="-db" type="text" optional="true" value="MSDB" label="the database to search in" help=""> - <expand macro="list_string_san"/> + <param argument="-db" type="text" optional="true" value="MSDB" label="the database to search in" help=""> + <expand macro="list_string_san" name="db"/> </param> - <param name="hits" argument="-hits" type="text" optional="true" value="AUTO" label="the number of hits to report" help=""> - <expand macro="list_string_san"/> + <param argument="-hits" type="text" optional="true" value="AUTO" label="the number of hits to report" help=""> + <expand macro="list_string_san" name="hits"/> </param> - <param name="cleavage" argument="-cleavage" type="select" optional="false" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)"> + <param argument="-cleavage" type="select" optional="true" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)"> <option value="Trypsin" selected="true">Trypsin</option> <option value="Arg-C">Arg-C</option> <option value="Asp-N">Asp-N</option> @@ -158,30 +156,30 @@ <option value="semiTrypsin">semiTrypsin</option> <option value="LysC+AspN">LysC+AspN</option> <option value="None">None</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="cleavage"/> </param> - <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="0" label="number of allowed missed cleavages" help=""/> - <param name="sig_threshold" argument="-sig_threshold" type="float" optional="true" value="0.05" label="significance threshold" help=""/> - <param name="pep_homol" argument="-pep_homol" type="float" optional="true" value="1.0" label="peptide homology threshold" help=""/> - <param name="pep_ident" argument="-pep_ident" type="float" optional="true" value="1.0" label="peptide ident threshold" help=""/> - <param name="pep_rank" argument="-pep_rank" type="integer" optional="true" value="1" label="peptide rank" help=""/> - <param name="prot_score" argument="-prot_score" type="float" optional="true" value="1.0" label="protein score" help=""/> - <param name="pep_score" argument="-pep_score" type="float" optional="true" value="1.0" label="peptide score" help=""/> - <param name="pep_exp_z" argument="-pep_exp_z" type="integer" optional="true" value="1" label="peptide expected charge" help=""/> - <param name="show_unassigned" argument="-show_unassigned" type="integer" optional="true" value="1" label="show_unassigned" help=""/> - <param name="first_dim_rt" argument="-first_dim_rt" type="float" optional="true" value="0.0" label="additional information which is added to every peptide identification as metavalue if set > 0" help=""/> - <param name="boundary" argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help=""> - <expand macro="list_string_san"/> + <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="0" label="number of allowed missed cleavages" help=""/> + <param argument="-sig_threshold" type="float" optional="true" value="0.05" label="significance threshold" help=""/> + <param argument="-pep_homol" type="float" optional="true" value="1.0" label="peptide homology threshold" help=""/> + <param argument="-pep_ident" type="float" optional="true" value="1.0" label="peptide ident threshold" help=""/> + <param argument="-pep_rank" type="integer" optional="true" value="1" label="peptide rank" help=""/> + <param argument="-prot_score" type="float" optional="true" value="1.0" label="protein score" help=""/> + <param argument="-pep_score" type="float" optional="true" value="1.0" label="peptide score" help=""/> + <param argument="-pep_exp_z" type="integer" optional="true" value="1" label="peptide expected charge" help=""/> + <param argument="-show_unassigned" type="integer" optional="true" value="1" label="show_unassigned" help=""/> + <param argument="-first_dim_rt" type="float" optional="true" value="0.0" label="additional information which is added to every peptide identification as metavalue if set > 0" help=""/> + <param argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help=""> + <expand macro="list_string_san" name="boundary"/> </param> - <param name="mass_type" argument="-mass_type" display="radio" type="select" optional="false" label="mass type" help=""> + <param argument="-mass_type" type="select" optional="true" label="mass type" help=""> <option value="Monoisotopic" selected="true">Monoisotopic</option> <option value="Average">Average</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="mass_type"/> </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"> @@ -189,9 +187,8 @@ </param> </inputs> <outputs> - <data name="out" label="${tool.name} on ${on_string}: out"> + <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"> <change_format> - <when input="out_type" value="idXML" format="idxml"/> <when input="out_type" value="mgf" format="mgf"/> </change_format> </data> @@ -199,13 +196,86 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_MascotAdapter"/> - <expand macro="manutest_MascotAdapter"/> + <tests><!-- TOPP_MascotAdapter_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="MascotAdapter_1_input.mzData"/> + <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta_frac="0.7"/> + <param name="out_type" value="mgf"/> + <param name="instrument" value="ESI-TRAP"/> + <param name="precursor_mass_tolerance" value="1.3"/> + <param name="peak_mass_tolerance" value="0.3"/> + <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/> + <param name="modifications" value=""Carboxymethyl (C)""/> + <param name="variable_modifications" value=""Variable_Modifications_TEST_1""/> + <param name="charges" value=""1+" "2+" "3+""/> + <param name="db" value="MSDB"/> + <param name="hits" value="AUTO"/> + <param name="cleavage" value="Trypsin"/> + <param name="missed_cleavages" value="1"/> + <param name="sig_threshold" value="0.05"/> + <param name="pep_homol" value="1.0"/> + <param name="pep_ident" value="1.0"/> + <param name="pep_rank" value="1"/> + <param name="prot_score" value="1.0"/> + <param name="pep_score" value="1.0"/> + <param name="pep_exp_z" value="1"/> + <param name="show_unassigned" value="1"/> + <param name="first_dim_rt" value="0.0"/> + <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/> + <param name="mass_type" value="Monoisotopic"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_MascotAdapter_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="MascotAdapter_2_input.mascotXML"/> + <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="out_type" value="idXML"/> + <param name="instrument" value="Default"/> + <param name="precursor_mass_tolerance" value="2.0"/> + <param name="peak_mass_tolerance" value="1.0"/> + <param name="taxonomy" value="All entries"/> + <param name="modifications" value=""/> + <param name="variable_modifications" value=""/> + <param name="charges" value=""1+" "2+" "3+""/> + <param name="db" value="MSDB"/> + <param name="hits" value="AUTO"/> + <param name="cleavage" value="Trypsin"/> + <param name="missed_cleavages" value="0"/> + <param name="sig_threshold" value="0.05"/> + <param name="pep_homol" value="1.0"/> + <param name="pep_ident" value="1.0"/> + <param name="pep_rank" value="1"/> + <param name="prot_score" value="1.0"/> + <param name="pep_score" value="1.0"/> + <param name="pep_exp_z" value="1"/> + <param name="show_unassigned" value="1"/> + <param name="first_dim_rt" value="0.0"/> + <param name="boundary" value=""/> + <param name="mass_type" value="Monoisotopic"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Annotates MS/MS spectra using Mascot. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MascotAdapter.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MascotAdapter.html]]></help> <expand macro="references"/> </tool>