Mercurial > repos > galaxyp > openms_openswathdecoygenerator
view OpenSwathDecoyGenerator.xml @ 13:496cf619e311 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:18:22 +0000 |
parents | 3769d3a7e9ba |
children | e833a89f25c8 |
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<?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: [Targeted Experiments]--> <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Generates decoys according to different models for a specific TraML</description> <macros> <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ @EXT_FOO@ #import re ## Preprocessing mkdir in && ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call set -o pipefail && @EXECUTABLE@ -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && @EXECUTABLE@ -ini @EXECUTABLE@.ctd -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' -out 'out/output.${out_type}' ## Postprocessing && mv 'out/output.${out_type}' '$out' #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv '@EXECUTABLE@.ctd' '$ctd_out' #end if]]></command> <configfiles> <inputs name="args_json" data_style="paths"/> <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/> <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help=""> <option value="TraML">traml</option> <option value="pqp">pqp</option> <option value="tsv">tabular (tsv)</option> <expand macro="list_string_san" name="out_type"/> </param> <param argument="-method" type="select" optional="true" label="Decoy generation method" help=""> <option value="shuffle" selected="true">shuffle</option> <option value="pseudo-reverse">pseudo-reverse</option> <option value="reverse">reverse</option> <option value="shift">shift</option> <expand macro="list_string_san" name="method"/> </param> <param argument="-decoy_tag" type="text" optional="true" value="DECOY_" label="decoy tag" help=""> <expand macro="list_string_san" name="decoy_tag"/> </param> <param argument="-switchKR" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to switch terminal K and R (to achieve different precursor mass)" help=""/> <expand macro="adv_opts_macro"> <param argument="-min_decoy_fraction" type="float" optional="true" value="0.8" label="Minimum fraction of decoy / target peptides and proteins" help=""/> <param argument="-aim_decoy_fraction" type="float" optional="true" value="1.0" label="Number of decoys the algorithm should generate (if unequal to 1, the algorithm will randomly select N peptides for decoy generation)" help=""/> <param argument="-shuffle_max_attempts" type="integer" optional="true" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/> <param argument="-shuffle_sequence_identity_threshold" type="float" optional="true" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help=""/> <param argument="-shift_precursor_mz_shift" type="float" optional="true" value="0.0" label="shift: precursor ion MZ shift in Thomson for shift decoy method" help=""/> <param argument="-shift_product_mz_shift" type="float" optional="true" value="20.0" label="shift: fragment ion MZ shift in Thomson for shift decoy method" help=""/> <param argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/> <param argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help=""> <expand macro="list_string_san" name="allowed_fragment_types"/> </param> <param argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help=""> <expand macro="list_string_san" name="allowed_fragment_charges"/> </param> <param argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/> <param argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/> <param argument="-separate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if decoys should not be appended to targets" 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=""> <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> <outputs> <data name="out" label="${tool.name} on ${on_string}: out" format="traml"> <change_format> <when input="out_type" value="pqp" format="pqp"/> <when input="out_type" value="tsv" format="tabular"/> </change_format> </data> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> <tests><!-- TOPP_OpenSwathDecoyGenerator_test_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="min_decoy_fraction" value="0.8"/> <param name="aim_decoy_fraction" value="1.0"/> <param name="shuffle_max_attempts" value="30"/> <param name="shuffle_sequence_identity_threshold" value="0.5"/> <param name="shift_precursor_mz_shift" value="0.0"/> <param name="shift_product_mz_shift" value="20.0"/> <param name="product_mz_threshold" value="0.025"/> <param name="allowed_fragment_types" value="b,y"/> <param name="allowed_fragment_charges" value="1,2,3,4"/> <param name="enable_detection_specific_losses" value="false"/> <param name="enable_detection_unspecific_losses" value="false"/> <param name="separate" value="true"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/> <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <param name="method" value="pseudo-reverse"/> <param name="decoy_tag" value="DECOY_"/> <param name="switchKR" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_OpenSwathDecoyGenerator_test_2 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="min_decoy_fraction" value="0.8"/> <param name="aim_decoy_fraction" value="1.0"/> <param name="shuffle_max_attempts" value="30"/> <param name="shuffle_sequence_identity_threshold" value="0.5"/> <param name="shift_precursor_mz_shift" value="0.0"/> <param name="shift_product_mz_shift" value="20.0"/> <param name="product_mz_threshold" value="0.8"/> <param name="allowed_fragment_types" value="b,y"/> <param name="allowed_fragment_charges" value="1,2,3,4"/> <param name="enable_detection_specific_losses" value="false"/> <param name="enable_detection_unspecific_losses" value="false"/> <param name="separate" value="false"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/> <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <param name="method" value="pseudo-reverse"/> <param name="decoy_tag" value="DECOY_"/> <param name="switchKR" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_OpenSwathDecoyGenerator_test_3 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="min_decoy_fraction" value="0.8"/> <param name="aim_decoy_fraction" value="1.0"/> <param name="shuffle_max_attempts" value="30"/> <param name="shuffle_sequence_identity_threshold" value="0.5"/> <param name="shift_precursor_mz_shift" value="0.0"/> <param name="shift_product_mz_shift" value="20.0"/> <param name="product_mz_threshold" value="0.025"/> <param name="allowed_fragment_types" value="b,y"/> <param name="allowed_fragment_charges" value="1,2,3,4"/> <param name="enable_detection_specific_losses" value="false"/> <param name="enable_detection_unspecific_losses" value="false"/> <param name="separate" value="true"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/> <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <param name="method" value="pseudo-reverse"/> <param name="decoy_tag" value="DECOY_"/> <param name="switchKR" value="false"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_OpenSwathDecoyGenerator_test_4 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="min_decoy_fraction" value="0.4"/> <param name="aim_decoy_fraction" value="1.0"/> <param name="shuffle_max_attempts" value="30"/> <param name="shuffle_sequence_identity_threshold" value="0.5"/> <param name="shift_precursor_mz_shift" value="0.0"/> <param name="shift_product_mz_shift" value="20.0"/> <param name="product_mz_threshold" value="0.025"/> <param name="allowed_fragment_types" value="b,y"/> <param name="allowed_fragment_charges" value="1,2,3,4"/> <param name="enable_detection_specific_losses" value="true"/> <param name="enable_detection_unspecific_losses" value="true"/> <param name="separate" value="true"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/> <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <param name="method" value="pseudo-reverse"/> <param name="decoy_tag" value="DECOY_"/> <param name="switchKR" value="true"/> <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[Generates decoys according to different models for a specific TraML For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathDecoyGenerator.html]]></help> <expand macro="references"/> </tool>