Mercurial > repos > galaxyp > openms_openswathmzmlfilecacher
diff OpenSwathMzMLFileCacher.xml @ 9:e7c43d17e3dc draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
---|---|
date | Wed, 09 Sep 2020 20:15:03 +0000 |
parents | b5121b003599 |
children | fc775d5aa321 |
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--- a/OpenSwathMzMLFileCacher.xml Fri May 17 09:44:13 2019 -0400 +++ b/OpenSwathMzMLFileCacher.xml Wed Sep 09 20:15:03 2020 +0000 @@ -1,56 +1,85 @@ <?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="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="2.3.0"> +<tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description> <macros> <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</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[OpenSwathMzMLFileCacher + <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}' -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_out_type: - -out_type - #if " " in str($param_out_type): - "$param_out_type" - #else - $param_out_type - #end if -#end if -#if $param_convert_back: - -convert_back -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +## Postprocessing +&& mv 'out/output.${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 name="param_in" type="data" format="mzml,sqMass" optional="False" label="Input mzML file" help="(-in) "/> - <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content <br>Note: that not all conversion paths work or make sense" help="(-out_type) "> - <option value="mzML">mzML</option> - <option value="sqMass">sqMass</option> + <param name="in" argument="-in" type="data" format="mzml,sqmass" optional="false" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/> + <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense"> + <option value="mzML">mzml</option> + <option value="sqMass">sqmass</option> + <expand macro="list_string_san"/> </param> - <param name="param_convert_back" display="radio" type="boolean" truevalue="-convert_back" falsevalue="" checked="false" optional="True" label="Convert back to mzML" help="(-convert_back) "/> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <param name="lossy_compression" argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help=""/> + <param name="full_meta" argument="-full_meta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write full meta information into sqMass file (may require large amounts of memory)" help=""/> + <expand macro="adv_opts_macro"> + <param name="lossy_mass_accuracy" argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/> + <param name="process_lowmemory" argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/> + <param name="lowmem_batchsize" argument="-lowmem_batchsize" type="integer" optional="true" min="0" value="500" label="The batch size of the low memory conversion" help=""/> + <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="ctd_out_FLAG">Output used ctd (ini) configuration file</option> + </param> </inputs> <outputs> - <data name="param_out" format="mzml"/> + <data name="out" label="${tool.name} on ${on_string}: out"> + <change_format> + <when input="out_type" value="mzML" format="mzml"/> + <when input="out_type" value="sqMass" format="sqmass"/> + </change_format> + </data> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>This tool caches the spectra and chromatogram data of an mzML to disk. + <tests> + <expand macro="autotest_OpenSwathMzMLFileCacher"/> + <expand macro="manutest_OpenSwathMzMLFileCacher"/> + </tests> + <help><![CDATA[This tool caches the spectra and chromatogram data of an mzML to disk. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_OpenSwathMzMLFileCacher.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_OpenSwathMzMLFileCacher.html]]></help> + <expand macro="references"/> </tool>