Mercurial > repos > galaxyp > openms_eicextractor
diff EICExtractor.xml @ 11:2bd3c83eed94 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
---|---|
date | Wed, 09 Sep 2020 12:58:22 +0000 |
parents | e8a9dc186db5 |
children | 0546885ddaf9 |
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--- a/EICExtractor.xml Fri May 17 10:01:56 2019 -0400 +++ b/EICExtractor.xml Wed Sep 09 12:58:22 2020 +0000 @@ -1,103 +1,112 @@ <?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: [Quantitation]--> -<tool id="EICExtractor" name="EICExtractor" version="2.3.0"> +<tool id="EICExtractor" name="EICExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Extracts intensities from dedicates positions in a LC/MS map</description> <macros> <token name="@EXECUTABLE@">EICExtractor</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[EICExtractor + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re --in - #for token in $param_in: - $token - #end for --in_header - #for token in $param_in_header: - $token - #end for -#if $param_pos: - -pos $param_pos -#end if -#if $param_rt_tol: - -rt_tol $param_rt_tol +## Preprocessing +mkdir in && +${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } +#if $in_header: + mkdir in_header && + ${ ' '.join(["ln -s '%s' 'in_header/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _]) } #end if -#if $param_mz_tol: - -mz_tol $param_mz_tol -#end if -#if $param_rt_collect: - -rt_collect $param_rt_collect -#end if -#if $param_out: - -out $param_out +mkdir pos && +ln -s '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' && +mkdir out && +#if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir auto_rt_out_debug_TIC && #end if -#if $param_auto_rt_enabled: - -auto_rt:enabled -#end if -#if $param_auto_rt_out_debug_TIC: - -auto_rt:out_debug_TIC $param_auto_rt_out_debug_TIC -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_out_separator: - -out_separator "$adv_opts.param_out_separator" -#end if - #if $adv_opts.param_force: - -force + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} +#if $in_header: + -in_header + ${' '.join(["'in_header/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _])} #end if - #if $adv_opts.param_auto_rt_FHWM: - -auto_rt:FHWM $adv_opts.param_auto_rt_FHWM +-pos +'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' +-out +'out/output.${gxy2omsext("csv")}' +#if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -auto_rt:out_debug_TIC + 'auto_rt_out_debug_TIC/output.${gxy2omsext("mzml")}' #end if - #if $adv_opts.param_auto_rt_SNThreshold: - -auto_rt:SNThreshold $adv_opts.param_auto_rt_SNThreshold +#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 + | tee '$stdout' #end if + +## Postprocessing +&& mv 'out/output.${gxy2omsext("csv")}' '$out' +#if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'auto_rt_out_debug_TIC/output.${gxy2omsext("mzml")}' '$auto_rt_out_debug_TIC' #end if -]]></command> +#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 name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input raw data file" help="(-in) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input raw data file" help=" select mzml data sets(s)"/> + <param name="in_header" argument="-in_header" type="data" format="txt" multiple="true" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/> + <param name="pos" argument="-pos" type="data" format="edta" optional="false" label="Input config file stating where to find signal" help=" select edta data sets(s)"/> + <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/> + <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/> + <param name="rt_collect" argument="-rt_collect" type="integer" optional="true" value="1" label="# of scans up & down in RT from highest point for ppm estimation in result" help=""/> + <section name="auto_rt" title="Parameters for automatic detection of injection RT peaks (no need to specify them in 'pos' input file)" help="" expanded="false"> + <param name="enabled" argument="-auto_rt:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help=""/> + <param name="FHWM" argument="-auto_rt:FHWM" type="float" optional="true" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="Gaussian smoothing filter with this width is applied to TIC"/> + <param name="SNThreshold" argument="-auto_rt:SNThreshold" type="float" optional="true" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="Higher thesholds will result in less peaks"/> + </section> + <expand macro="adv_opts_macro"> + <param name="out_separator" argument="-out_separator" type="text" optional="true" value="," label="Separator character for output CSV file" help=""> + <expand macro="list_string_san"/> + </param> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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> + </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <option value="out_debug_TIC_FLAG">out_debug_TIC (Optional output file (for first input) containing the smoothed TIC, S/N levels and picked RT positions)</option> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> - <param name="param_in_header" type="data" format="txt" multiple="true" optional="True" size="30" label="[for Waters data only] Read additional information from _HEADER.TXT" help="(-in_header) Provide one for each raw input file"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_pos" type="data" format="tabular" optional="False" label="Input config file stating where to find signal" help="(-pos) "/> - <param name="param_rt_tol" type="float" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help="(-rt_tol) "/> - <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol) "/> - <param name="param_rt_collect" type="integer" value="1" label="# of scans up & down in RT from highest point for ppm estimation in result" help="(-rt_collect) "/> - <param name="param_auto_rt_enabled" display="radio" type="boolean" truevalue="-auto_rt:enabled" falsevalue="" checked="false" optional="True" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help="(-enabled) "/> - <expand macro="advanced_options"> - <param name="param_out_separator" type="text" size="30" value="," label="Separator character for output CSV file" help="(-out_separator) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> - <param name="param_auto_rt_FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="(-FHWM) Gaussian smoothing filter with this width is applied to TIC"/> - <param name="param_auto_rt_SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="(-SNThreshold) Higher thesholds will result in less peaks"/> - </expand> </inputs> <outputs> - <data name="param_out" format="tabular"/> - <data name="param_auto_rt_out_debug_TIC" format="mzml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/> + <data name="auto_rt_out_debug_TIC" label="${tool.name} on ${on_string}: auto_rt:out_debug_TIC" format="mzml"> + <filter>OPTIONAL_OUTPUTS is not None and "out_debug_TIC_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Extracts intensities from dedicates positions in a LC/MS map + <tests> + <expand macro="autotest_EICExtractor"/> + <expand macro="manutest_EICExtractor"/> + </tests> + <help><![CDATA[Extracts intensities from dedicates positions in a LC/MS map -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_EICExtractor.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_EICExtractor.html]]></help> + <expand macro="references"/> </tool>