Mercurial > repos > galaxyp > openms_idfileconverter
diff IDFileConverter.xml @ 3:066cf4d993f5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
| author | galaxyp |
|---|---|
| date | Wed, 09 Aug 2017 09:10:41 -0400 |
| parents | 5588e443a7db |
| children | 1dcffdad49c0 |
line wrap: on
line diff
--- a/IDFileConverter.xml Thu Apr 27 13:23:15 2017 -0400 +++ b/IDFileConverter.xml Wed Aug 09 09:10:41 2017 -0400 @@ -1,7 +1,7 @@ <?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 CTD2Galaxy.--> <!--Proposed Tool Section: [ID Processing]--> -<tool id="IDFileConverter" name="IDFileConverter" version="2.1.0"> +<tool id="IDFileConverter" name="IDFileConverter" version="2.2.0"> <description>Converts identification engine file formats.</description> <macros> <token name="@EXECUTABLE@">IDFileConverter</token> @@ -11,68 +11,71 @@ <expand macro="stdio"/> <expand macro="requirements"/> <command><![CDATA[ - - ## check input file type - #set $in_type = $param_in.ext + +## check input file type +#set $in_type = $param_in.ext - ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files - ln -s '$param_in' 'param_in.${in_type}' && - - IDFileConverter +## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files +ln -s '$param_in' 'param_in.${in_type}' && + +IDFileConverter - #if $param_in: - -in 'param_in.${in_type}' - #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_mz_file: - -mz_file $param_mz_file +#if $param_in: + -in 'param_in.${in_type}' +#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 - #if $param_mz_name: - -mz_name "$param_mz_name" - #end if - #if $param_peptideprophet_analyzed: - -peptideprophet_analyzed +#end if +#if $param_mz_file: + -mz_file $param_mz_file +#end if +#if $param_mz_name: + -mz_name "$param_mz_name" +#end if +#if $param_peptideprophet_analyzed: + -peptideprophet_analyzed +#end if +#if $param_score_type: + -score_type + #if " " in str($param_score_type): + "$param_score_type" + #else + $param_score_type #end if - #if $param_score_type: - -score_type - #if " " in str($param_score_type): - "$param_score_type" - #else - $param_score_type - #end if - #end if - #if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_ignore_proteins_per_peptide: - -ignore_proteins_per_peptide - #end if - #if $adv_opts.param_scan_regex: - -scan_regex "$adv_opts.param_scan_regex" - #end if - #if $adv_opts.param_force: - -force - #end if - #end if - ]]> +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_ignore_proteins_per_peptide: + -ignore_proteins_per_peptide +#end if + #if $adv_opts.param_scan_regex: + -scan_regex "$adv_opts.param_scan_regex" +#end if + #if $adv_opts.param_no_spectra_data_override: + -no_spectra_data_override +#end if + #if $adv_opts.param_force: + -force +#end if +#end if +]]> </command> <inputs> - <param name="param_in" type="data" format="tabular,mzid,pepxml,idxml" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: <br>- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), <br>- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), <br>- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), <br>- for Sequest results, a directory containing .out files. <br>"/> + <param name="param_in" type="data" format="pepxml,protXML,mascotXML,omssaXML,xml,psms,tabular,idxml,mzid" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: <br>- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), <br>- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), <br>- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), <br>- for Sequest results, a directory containing .out files. <br>"/> <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) "> <option value="idXML">idXML</option> <option value="mzid">mzid</option> <option value="pepXML">pepXML</option> <option value="FASTA">FASTA</option> </param> - <param name="param_mz_file" type="data" format="mzxml,mzml" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, Percolator only] Retention times will be looked up in this file" help="(-mz_file) "/> + <param name="param_mz_file" type="data" format="mzml,mzxml,mzData" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file" help="(-mz_file) "/> <param name="param_mz_name" type="text" size="30" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="(-mz_name) Only necessary if different from 'mz_file'"> <sanitizer> <valid initial="string.printable"> @@ -97,6 +100,7 @@ </valid> </sanitizer> </param> + <param name="param_no_spectra_data_override" display="radio" type="boolean" truevalue="-no_spectra_data_override" falsevalue="" checked="false" optional="True" label="[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated" help="(-no_spectra_data_override) Use only if you are sure it is absolutely the same mz_file as used for identification"/> <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> </expand> </inputs>