Mercurial > repos > galaxyp > openms_databasefilter
diff DatabaseFilter.xml @ 14:0878a55de9e7 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
---|---|
date | Thu, 01 Dec 2022 19:17:07 +0000 |
parents | 0c98acedb17a |
children | 2f7a8b58314e |
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--- a/DatabaseFilter.xml Fri Nov 06 20:11:58 2020 +0000 +++ b/DatabaseFilter.xml Thu Dec 01 19:17:07 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="DatabaseFilter" name="DatabaseFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="DatabaseFilter" name="DatabaseFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Filters a protein database (FASTA format) based on identified proteins</description> <macros> <token name="@EXECUTABLE@">DatabaseFilter</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -45,17 +43,17 @@ <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="fasta" optional="false" label="Input FASTA file, containing a database" help=" select fasta data sets(s)"/> - <param name="id" argument="-id" type="data" format="idxml,mzid" optional="false" label="Input file containing identified peptides and proteins" help=" select idxml,mzid data sets(s)"/> - <param name="method" argument="-method" display="radio" type="select" optional="false" label="Switch between white-/blacklisting" help=""> + <param argument="-in" type="data" format="fasta" optional="false" label="Input FASTA file, containing a database" help=" select fasta data sets(s)"/> + <param argument="-id" type="data" format="idxml,mzid" optional="false" label="Input file containing identified peptides and proteins" help=" select idxml,mzid data sets(s)"/> + <param argument="-method" type="select" optional="true" label="Switch between white-/blacklisting" help=""> <option value="whitelist" selected="true">whitelist</option> <option value="blacklist">blacklist</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="method"/> </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"> @@ -68,13 +66,78 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_DatabaseFilter"/> - <expand macro="manutest_DatabaseFilter"/> + <tests><!-- UTILS_DatabaseFilter_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="DatabaseFilter_1.fasta"/> + <param name="id" value="DatabaseFilter_1.idXML"/> + <param name="method" value="whitelist"/> + <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- UTILS_DatabaseFilter_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="DatabaseFilter_1.fasta"/> + <param name="id" value="DatabaseFilter_1.idXML"/> + <param name="method" value="blacklist"/> + <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- UTILS_DatabaseFilter_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="DatabaseFilter_3.fasta"/> + <param name="id" value="DatabaseFilter_3.mzid"/> + <param name="method" value="whitelist"/> + <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- UTILS_DatabaseFilter_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="DatabaseFilter_3.fasta"/> + <param name="id" value="DatabaseFilter_3.mzid"/> + <param name="method" value="blacklist"/> + <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> + <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[Filters a protein database (FASTA format) based on identified proteins -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_DatabaseFilter.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DatabaseFilter.html]]></help> <expand macro="references"/> </tool>