Mercurial > repos > galaxyp > openms_openswathdiaprescoring
view OpenSwathDIAPreScoring.xml @ 11:c99d5004b74f 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 19:20:01 +0000 |
parents | e6ba7a995b35 |
children | 986d14ec9394 |
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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="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Scoring spectra using the DIA scores.</description> <macros> <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</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 tr && ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && mkdir swath_files_cond.swath_files && #if $swath_files_cond.swath_files_select == "no" mkdir ${' '.join(["'swath_files_cond.swath_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} && ${' '.join(["ln -s '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])} #else ln -s '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' && #end if mkdir output_files && mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} && ## Main program call set -o pipefail && @EXECUTABLE@ -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && @EXECUTABLE@ -ini @EXECUTABLE@.ctd -tr 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' -swath_files #if $swath_files_cond.swath_files_select == "no" ${' '.join(["'swath_files_cond.swath_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])} #else 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' #end if -output_files ${' '.join(["'output_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("tabular")) for i, f in enumerate($swath_files_cond.swath_files) if f])} ## Postprocessing ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(gext)s' 'output_files/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("tabular")} for i, f in enumerate($swath_files_cond.swath_files) if f])} #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="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/> <conditional name="swath_files_cond"> <param name="swath_files_select" type="select" label="Run tool in batch mode for -swath_files"> <option value="no">No: process all datasets jointly</option> <option value="yes">Yes: process each dataset in an independent job</option> </param> <when value="no"> <param argument="-swath_files" type="data" format="mzml" multiple="true" optional="false" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/> </when> <when value="yes"> <param argument="-swath_files" type="data" format="mzml" multiple="false" optional="false" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/> </when> </conditional> <param argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/> <expand macro="adv_opts_macro"> <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> <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files"> <discover_datasets directory="output_files" recurse="true" format="tabular" pattern="__name__"/> </collection> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> <tests><!-- data from a test that included all the needed test files --> <test> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> <output_collection name="output_files" count="1"> <element name="OpenSwathAnalyzer_2_swathfile_mzML" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> </output_collection> </test> <!-- test with two inputs (actually the same file .. symlinked) --> <test> <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/> <output_collection name="output_files" count="2"> <element name="OpenSwathDIAPreScoring_in1_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/> <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/> </output_collection> </test> </tests> <help><![CDATA[Scoring spectra using the DIA scores. For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathDIAPreScoring.html]]></help> <expand macro="references"/> </tool>