Mercurial > repos > bgruening > openms
diff IDMassAccuracy.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
| author | bgruening |
|---|---|
| date | Wed, 27 Jan 2016 10:06:49 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/IDMassAccuracy.xml Wed Jan 27 10:06:49 2016 -0500 @@ -0,0 +1,138 @@ +<?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: [Utilities]--> + <tool id="IDMassAccuracy" name="IDMassAccuracy" version="2.0.0"> + <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description> + <macros> + <token name="@EXECUTABLE@">IDMassAccuracy</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>IDMassAccuracy + +-in + #for token in $param_in: + $token + #end for +-id_in + #for token in $param_id_in: + $token + #end for +#if $param_precursor_out: + -precursor_out $param_precursor_out +#end if + +#if $rep_param_precursor_columns: +-precursor_columns + #for token in $rep_param_precursor_columns: + #if " " in str(token): + "$token.param_precursor_columns" + #else + $token.param_precursor_columns + #end if + #end for +#end if +#if $param_precursor_error_ppm: + -precursor_error_ppm +#end if +#if $param_fragment_out: + -fragment_out $param_fragment_out +#end if + +#if $rep_param_fragment_columns: +-fragment_columns + #for token in $rep_param_fragment_columns: + #if " " in str(token): + "$token.param_fragment_columns" + #else + $token.param_fragment_columns + #end if + #end for +#end if +#if $param_fragment_error_ppm: + -fragment_error_ppm +#end if +#if $param_fragment_mass_tolerance: + -fragment_mass_tolerance $param_fragment_mass_tolerance +#end if +#if $param_separator: + -separator "$param_separator" +#end if +-threads \${GALAXY_SLOTS:-24} +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_number_of_bins: + -number_of_bins $adv_opts.param_number_of_bins +#end if + #if $adv_opts.param_generate_gnuplot_scripts: + -generate_gnuplot_scripts +#end if + #if $adv_opts.param_force: + -force +#end if +#end if +</command> + <inputs> + <param format="mzml" help="(-in) " label="Input mzML file list, containing the spectra" multiple="true" name="param_in" optional="False" size="30" type="data"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param format="xml" help="(-id_in) " label="Input idXML file list, containing the identifications" multiple="true" name="param_id_in" optional="False" size="30" type="data"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <repeat max="1" min="0" name="rep_param_precursor_columns" title="param_precursor_columns"> + <param help="(-precursor_columns) " label="Columns which will be written to the output file" name="param_precursor_columns" size="30" type="text" value="MassDifference"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param checked="false" falsevalue="" help="(-precursor_error_ppm) " label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" name="param_precursor_error_ppm" optional="True" truevalue="-precursor_error_ppm" type="boolean"/> + <repeat max="1" min="0" name="rep_param_fragment_columns" title="param_fragment_columns"> + <param help="(-fragment_columns) " label="Columns which will be written to the output file" name="param_fragment_columns" size="30" type="text" value="MassDifference"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param checked="false" falsevalue="" help="(-fragment_error_ppm) " label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" name="param_fragment_error_ppm" optional="True" truevalue="-fragment_error_ppm" type="boolean"/> + <param help="(-fragment_mass_tolerance) " label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" name="param_fragment_mass_tolerance" type="float" value="0.5"/> + <param help="(-separator) " label="character which should be used to separate the columns in the output files" name="param_separator" size="30" type="text" value=" "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <expand macro="advanced_options"> + <param help="(-number_of_bins) " label="Number of bins that should be used to calculate the histograms for the fitting" min="10" name="param_number_of_bins" optional="True" type="integer" value="100"/> + <param checked="false" falsevalue="" help="(-generate_gnuplot_scripts) The options 'precursor_out' and 'fragment_out' must be set to take this effect" label="If this option is set to true, the distributions and the fits are used to generate a gnuplot script, that can be used to generate plots" name="param_generate_gnuplot_scripts" optional="True" truevalue="-generate_gnuplot_scripts" type="boolean"/> + <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> + </expand> + </inputs> + <outputs> + <data format="tabular" name="param_precursor_out"/> + <data format="tabular" name="param_fragment_out"/> + </outputs> + <help>Calculates a distribution of the mass error from given mass spectra and IDs. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDMassAccuracy.html</help> + </tool>