Mercurial > repos > galaxyp > openms_filemerger
diff FileMerger.xml @ 15:b2fc8da99bcc draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:10:42 +0000 |
| parents | 8b871a67ba56 |
| children | 0643576e7f51 |
line wrap: on
line diff
--- a/FileMerger.xml Fri Nov 06 19:47:14 2020 +0000 +++ b/FileMerger.xml Thu Dec 01 19:10:42 2022 +0000 @@ -1,13 +1,11 @@ <?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="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="FileMerger" name="FileMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <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="requirements"/> <expand macro="stdio"/> @@ -16,11 +14,17 @@ #import re ## Preprocessing -mkdir in && -${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } +mkdir in_cond.in && +#if $in_cond.in_select == "no" +mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && +${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +#else +ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +#end if mkdir out && #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir rt_concat_trafo_out && + mkdir ${' '.join(["'rt_concat_trafo_out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && #end if ## Main program call @@ -30,12 +34,16 @@ 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 $in_cond.in_select == "no" +${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +#else +'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' +#end if -out 'out/output.${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 _])} + ${' '.join(["'rt_concat_trafo_out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("trafoxml")) for i, f in enumerate($in_cond.in) if f])} #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' @@ -44,7 +52,7 @@ ## 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 _])} + ${' '.join(["&& mv -n 'rt_concat_trafo_out/%(bn)s/%(id)s.%(gext)s' 'rt_concat_trafo_out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("trafoxml")} for i, f in enumerate($in_cond.in) if f])} #end if #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv '@EXECUTABLE@.ctd' '$ctd_out' @@ -54,7 +62,18 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <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)"/> + <conditional name="in_cond"> + <param name="in_select" type="select" label="Run tool in batch mode for -in"> + <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="-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)"/> + </when> + <when value="yes"> + <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" multiple="false" optional="false" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/> + </when> + </conditional> <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> @@ -62,11 +81,11 @@ <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)"> + <param 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 argument="-append_method" type="select" optional="true" label="(ConsensusXML-only) Append quantitative information about features row-wise or column-wise" help="- 'append_rows' is usually used when the inputs come from the same MS run (e.g. caused by manual splitting or multiple algorithms on the same file). - 'append_cols' when you want to combine consensusXMLs from e.g. different fractions to be summarized in ProteinQuantifier or jointly exported with MzTabExporter"> <option value="append_rows" selected="true">append_rows</option> <option value="append_cols">append_cols</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="append_method"/> </param> <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"/> @@ -74,15 +93,15 @@ <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"/> + <expand macro="list_float_valsan" name="rt_custom"/> </param> <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="Overrides 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 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"> @@ -91,9 +110,8 @@ </param> </inputs> <outputs> - <data name="out" label="${tool.name} on ${on_string}: out"> + <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"> <change_format> - <when input="out_type" value="consensusXML" format="consensusxml"/> <when input="out_type" value="fasta" format="fasta"/> <when input="out_type" value="featureXML" format="featurexml"/> <when input="out_type" value="mzML" format="mzml"/> @@ -101,20 +119,308 @@ </change_format> </data> <collection type="list" name="rt_concat_trafo_out" label="${tool.name} on ${on_string}: rt_concat:trafo_out"> - <discover_datasets directory="rt_concat.trafo_out" format="trafoxml" pattern="__name__"/> + <discover_datasets directory="rt_concat_trafo_out" recurse="true" format="trafoxml" pattern="__name__"/> <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter> </collection> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_FileMerger"/> - <expand macro="manutest_FileMerger"/> + <tests><!-- TOPP_FileMerger_2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/> + </conditional> + <param name="out_type" value="mzML"/> + <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value="5.0 10.0"/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileMerger_3 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/> + </conditional> + <param name="out_type" value="mzML"/> + <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="true"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileMerger_4 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/> + </conditional> + <param name="out_type" value="mzML"/> + <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileMerger_5 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/> + </conditional> + <param name="out_type" value="mzML"/> + <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="true"/> + <param name="ms_level" value="2"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileMerger_6 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/> + </conditional> + <param name="out_type" value="mzML"/> + <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileMerger_7 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/> + </conditional> + <param name="out_type" value="featureXML"/> + <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileMerger_8 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/> + </conditional> + <param name="out_type" value="consensusXML"/> + <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileMerger_9 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/> + </conditional> + <param name="out_type" value="traML"/> + <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileMerger_10 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/> + </conditional> + <param name="out_type" value="mzML"/> + <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_rows"/> + <section name="rt_concat"> + <param name="gap" value="10.0"/> + </section> + <output_collection name="rt_concat_trafo_out" count="2"/> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileMerger_11 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/> + </conditional> + <param name="out_type" value="consensusXML"/> + <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> + <param name="annotate_file_origin" value="false"/> + <param name="append_method" value="append_cols"/> + <section name="rt_concat"> + <param name="gap" value="0.0"/> + </section> + <section name="raw"> + <param name="rt_auto" value="false"/> + <param name="rt_custom" value=""/> + <param name="rt_filename" value="false"/> + <param name="ms_level" value="0"/> + </section> + <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[Merges several MS files into one file. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FileMerger.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileMerger.html]]></help> <expand macro="references"/> </tool>