Mercurial > repos > galaxyp > openms_idmapper
diff IDMapper.xml @ 16:ea02403ff738 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 21:39:26 +0000 |
| parents | adca857b4884 |
| children |
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--- a/IDMapper.xml Thu Dec 01 19:05:34 2022 +0000 +++ b/IDMapper.xml Fri Jun 14 21:39:26 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: [ID Processing]--> +<!--Proposed Tool Section: [Identification Processing]--> <tool id="IDMapper" name="IDMapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Assigns protein/peptide identifications to features or consensus features.</description> + <description>Assigns protein/peptide identifications to features or consensus features</description> <macros> <token name="@EXECUTABLE@">IDMapper</token> <import>macros.xml</import> @@ -15,13 +14,13 @@ ## Preprocessing mkdir id && -ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && +cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && mkdir in && -ln -s '$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 $spectra._in: mkdir spectra.in && - ln -s '$spectra._in' 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)' && + cp '$spectra._in' 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)' && #end if ## Main program call @@ -51,16 +50,16 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-id" type="data" format="idxml,mzid" optional="false" label="Protein/peptide identifications file" help=" select idxml,mzid data sets(s)"/> - <param argument="-in" type="data" format="consensusxml,featurexml,mzq" optional="false" label="Feature map/consensus map file" help=" select consensusxml,featurexml,mzq data sets(s)"/> - <param argument="-rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/> - <param argument="-mz_tolerance" type="float" optional="true" min="0.0" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/> - <param argument="-mz_measure" type="select" optional="true" label="Unit of 'mz_tolerance'" help=""> + <param argument="-id" type="data" format="idxml,mzid" label="Protein/peptide identifications file" help=" select idxml,mzid data sets(s)"/> + <param argument="-in" type="data" format="consensusxml,featurexml,mzq" label="Feature map/consensus map file" help=" select consensusxml,featurexml,mzq data sets(s)"/> + <param argument="-rt_tolerance" type="float" min="0.0" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/> + <param argument="-mz_tolerance" type="float" min="0.0" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/> + <param argument="-mz_measure" type="select" label="Unit of 'mz_tolerance'" help=""> <option value="ppm" selected="true">ppm</option> <option value="Da">Da</option> <expand macro="list_string_san" name="mz_measure"/> </param> - <param argument="-mz_reference" type="select" optional="true" label="Source of m/z values for peptide identifications" help="If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',. masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)"> + <param argument="-mz_reference" type="select" label="Source of m/z values for peptide identifications" help="If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',. masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)"> <option value="precursor">precursor</option> <option value="peptide" selected="true">peptide</option> <expand macro="list_string_san" name="mz_reference"/> @@ -79,7 +78,7 @@ <expand macro="adv_opts_macro"> <param argument="-ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" help=""/> <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> @@ -93,7 +92,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_IDMapper_1 --> + <tests> + <!-- TOPP_IDMapper_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="ignore_charge" value="true"/> @@ -102,7 +102,7 @@ </section> <param name="id" value="IDMapper_1_input.idXML"/> <param name="in" value="IDMapper_1_input.featureXML"/> - <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="IDMapper_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <param name="rt_tolerance" value="5.0"/> <param name="mz_tolerance" value="1.0"/> <param name="mz_measure" value="Da"/> @@ -122,6 +122,9 @@ <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_IDMapper_2 --> <test expect_num_outputs="2"> @@ -132,7 +135,7 @@ </section> <param name="id" value="IDMapper_2_input.idXML"/> <param name="in" value="IDMapper_2_input.consensusXML"/> - <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <output name="out" value="IDMapper_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <param name="rt_tolerance" value="5.0"/> <param name="mz_tolerance" value="1.0"/> <param name="mz_measure" value="Da"/> @@ -152,6 +155,9 @@ <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_IDMapper_3 --> <test expect_num_outputs="2"> @@ -162,7 +168,7 @@ </section> <param name="id" value="IDMapper_3_input.idXML"/> <param name="in" value="IDMapper_3_input.featureXML"/> - <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="IDMapper_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <param name="rt_tolerance" value="4.0"/> <param name="mz_tolerance" value="3.0"/> <param name="mz_measure" value="ppm"/> @@ -182,75 +188,14 @@ <is_valid_xml/> </assert_contents> </output> - </test> - <!-- TOPP_IDMapper_4 --> - <test expect_num_outputs="2"> - <section name="adv_opts"> - <param name="ignore_charge" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </section> - <param name="id" value="IDMapper_4_input.idXML"/> - <param name="in" value="IDMapper_4_input.featureXML"/> - <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> - <param name="rt_tolerance" value="10.0"/> - <param name="mz_tolerance" value="20.0"/> - <param name="mz_measure" value="ppm"/> - <param name="mz_reference" value="peptide"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="true"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"> - <param name="_in" value="IDMapper_4_input.mzML"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <!-- TOPP_IDMapper_5 --> - <test expect_num_outputs="2"> - <section name="adv_opts"> - <param name="ignore_charge" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </section> - <param name="id" value="IDMapper_5_input.idXML"/> - <param name="in" value="IDMapper_5_input.featureXML"/> - <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> - <param name="rt_tolerance" value="20.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_measure" value="ppm"/> - <param name="mz_reference" value="peptide"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="false"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"> - <param name="_in" value="IDMapper_5_input.mzML"/> - </section> - <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> </tests> <help><![CDATA[Assigns protein/peptide identifications to features or consensus features. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDMapper.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDMapper.html]]></help> <expand macro="references"/> </tool>