Mercurial > repos > galaxyp > openms_filemerger
diff FileMerger.xml @ 11:1dfc532aadd1 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
| author | galaxyp |
|---|---|
| date | Thu, 27 Aug 2020 19:42:01 -0400 |
| parents | 7186f4354d84 |
| children | 8b871a67ba56 |
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--- a/FileMerger.xml Fri May 17 10:15:30 2019 -0400 +++ b/FileMerger.xml Thu Aug 27 19:42:01 2020 -0400 @@ -1,101 +1,120 @@ <?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: [File Handling]--> -<tool id="FileMerger" name="FileMerger" version="2.3.0"> +<tool id="FileMerger" name="FileMerger" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Merges several MS files into one file.</description> <macros> <token name="@EXECUTABLE@">FileMerger</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[FileMerger + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re --in - #for token in $param_in: - $token - #end for -#if $param_out: - -out $param_out -#end if -#if $param_annotate_file_origin: - -annotate_file_origin -#end if -#if $param_rt_concat_gap: - -rt_concat:gap $param_rt_concat_gap +## Preprocessing +mkdir in && +${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } +mkdir out && +#if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir rt_concat_trafo_out && #end if -#if $rep_param_rt_concat_trafo_out: --rt_concat:trafo_out - #for token in $rep_param_rt_concat_trafo_out: - #if " " in str(token): - "$token.param_rt_concat_trafo_out" - #else - $token.param_rt_concat_trafo_out - #end if - #end for +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__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 $in if _])} +-out +'out/output.${out_type}' +#if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -rt_concat:trafo_out + ${' '.join(["'rt_concat_trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])} #end if -#if $param_raw_rt_auto: - -raw:rt_auto +#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 + | tee '$stdout' #end if -#if $rep_param_raw_rt_custom: --raw:rt_custom - #for token in $rep_param_raw_rt_custom: - #if " " in str(token): - "$token.param_raw_rt_custom" - #else - $token.param_raw_rt_custom - #end if - #end for +## Postprocessing +&& mv 'out/output.${out_type}' '$out' +#if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'rt_concat_trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $rt_concat_trafo_out if _])} #end if -#if $param_raw_rt_filename: - -raw:rt_filename -#end if -#if $param_raw_ms_level: - -raw:ms_level $param_raw_ms_level -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#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="mzData,mzxml,mzml,dta,dta2d,mgf,featurexml,consensusxml,fid,traml,fasta" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" multiple="true" optional="false" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/> + <param name="out_type" type="select" optional="false" label="File type of output out (Output file)"> + <option value="mzML">mzml</option> + <option value="featureXML">featurexml</option> + <option value="consensusXML">consensusxml</option> + <option value="traML">traml</option> + <option value="fasta">fasta</option> + </param> + <param name="annotate_file_origin" argument="-annotate_file_origin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original filename in each feature using meta value "file_origin" (for featureXML and consensusXML only)" help=""/> + <param name="append_method" argument="-append_method" display="radio" type="select" optional="false" label="Append consensusMaps rowise or colwise" help="(Please use colwise for the MSstatsConverter)"> + <option value="append_rows" selected="true">append_rows</option> + <option value="append_cols">append_cols</option> + <expand macro="list_string_san"/> </param> - <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each feature using meta value "file_origin" (for featureXML and consensusXML only)" help="(-annotate_file_origin) "/> - <param name="param_rt_concat_gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="(-gap) RT concatenation is enabled if a value > 0 is set"/> - <param name="param_raw_rt_auto" display="radio" type="boolean" truevalue="-raw:rt_auto" falsevalue="" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto) "/> - <repeat name="rep_param_raw_rt_custom" min="0" title="param_raw_rt_custom"> - <param name="param_raw_rt_custom" type="text" size="30" value="0" label="List of custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <section name="rt_concat" title="Options for concatenating files in the retention time (RT) dimension" help="The RT ranges of inputs are adjusted so they don't overlap in the merged file (traML input not supported)" expanded="false"> + <param name="gap" argument="-rt_concat:gap" type="float" optional="true" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="RT concatenation is enabled if a value > 0 is set"/> + </section> + <section name="raw" title="Options for raw data input/output (primarily for DTA files)" help="" expanded="false"> + <param name="rt_auto" argument="-raw:rt_auto" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign retention times automatically (integers starting at 1)" help=""/> + <param name="rt_custom" argument="-raw:rt_custom" type="text" optional="true" value="" label="List of custom retention times that are assigned to the files" help="The number of given retention times must be equal to the number of input files (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_float_valsan"/> </param> - </repeat> - <param name="param_raw_rt_filename" display="radio" type="boolean" truevalue="-raw:rt_filename" falsevalue="" checked="false" optional="True" label="Try to guess the retention time of a file based on the filename. This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number," help="(-rt_filename) e.g. 'my_spectrum_rt2795.15.dta'"/> - <param name="param_raw_ms_level" type="integer" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="(-ms_level) This option is useful for DTA files which do not contain MS level information"/> - <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="rt_filename" argument="-raw:rt_filename" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to guess the retention time of a file based on the filename" help="This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number, e.g. 'my_spectrum_rt2795.15.dta'"/> + <param name="ms_level" argument="-raw:ms_level" type="integer" optional="true" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="This option is useful for DTA files which do not contain MS level information"/> + </section> + <expand macro="adv_opts_macro"> + <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="trafo_out_FLAG">trafo_out (If 1 or higher, this number is assigned to spectra as the MS level)</option> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> + </param> </inputs> <outputs> - <data name="param_out" format="featurexml"/> - <data name="param_rt_concat_trafo_out" format="trafoxml"/> + <data name="out" label="${tool.name} on ${on_string}: out"> + <change_format> + <when input="out_type" value="consensusXML" format="consensusxml"/> + <when input="out_type" value="fasta" format="fasta"/> + <when input="out_type" value="featureXML" format="featurexml"/> + <when input="out_type" value="mzML" format="mzml"/> + <when input="out_type" value="traML" format="traml"/> + </change_format> + </data> + <collection type="list" name="rt_concat_trafo_out" label="${tool.name} on ${on_string}: rt_concat:trafo_out"> + <discover_datasets directory="rt_concat.trafo_out" format="trafoxml" pattern="__name__"/> + <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </collection> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Merges several MS files into one file. + <tests> + <expand macro="autotest_FileMerger"/> + <expand macro="manutest_FileMerger"/> + </tests> + <help><![CDATA[Merges several MS files into one file. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FileMerger.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_FileMerger.html]]></help> + <expand macro="references"/> </tool>