Mercurial > repos > galaxyp > openms_idrtcalibration
view IDRTCalibration.xml @ 14:7ff821b34ebc 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 19:25:24 +0000 |
parents | 28805cf9b024 |
children | f7226e34dc70 |
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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: [ID Processing]--> <tool id="IDRTCalibration" name="IDRTCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description> <macros> <token name="@EXECUTABLE@">IDRTCalibration</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($in.ext)' -out 'out/output.${gxy2omsext("idxml")}' ## Postprocessing && mv 'out/output.${gxy2omsext("idxml")}' '$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="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/> <param argument="-calibrant_1_reference" type="float" optional="true" value="0.1" label="The RT of the first calibrant in the reference file" help=""/> <param argument="-calibrant_2_reference" type="float" optional="true" value="0.9" label="The RT of the second calibrant in the reference file" help=""/> <param argument="-calibrant_1_input" type="float" optional="true" value="-1.0" label="The RT of the first calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/> <param argument="-calibrant_2_input" type="float" optional="true" value="-1.0" label="The RT of the second calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/> <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> <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> <tests><!-- TOPP_IDRTCalibration_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="IDRTCalibration_1_input.idXML"/> <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> <param name="calibrant_1_reference" value="0.1"/> <param name="calibrant_2_reference" value="0.9"/> <param name="calibrant_1_input" value="10.0"/> <param name="calibrant_2_input" value="90.0"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_IDRTCalibration_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="degenerated_empty.idXML"/> <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> <param name="calibrant_1_reference" value="0.1"/> <param name="calibrant_2_reference" value="0.9"/> <param name="calibrant_1_input" value="10.0"/> <param name="calibrant_2_input" value="90.0"/> <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[Can be used to calibrate RTs of peptide hits linearly to standards. For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRTCalibration.html]]></help> <expand macro="references"/> </tool>