Mercurial > repos > bgruening > openms
diff MassCalculator.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 | 3d84209d3178 |
| children |
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--- a/MassCalculator.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MassCalculator.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,59 +1,132 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="MassCalculator" name="MassCalculator" version="1.12.0"> - <description>Calculates masses and mass-to-charge ratios of peptide sequences</description> - <macros> - <token name="@EXECUTABLE@">MassCalculator</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>MassCalculator +<?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="MassCalculator" name="MassCalculator" version="2.0.0"> + <description>Calculates masses and mass-to-charge ratios of peptide sequences</description> + <macros> + <token name="@EXECUTABLE@">MassCalculator</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>MassCalculator + +#if $param_in: + -in $param_in +#end if + +#if $rep_param_in_seq: +-in_seq + #for token in $rep_param_in_seq: + #if " " in str(token): + "$token.param_in_seq" + #else + $token.param_in_seq + #end if + #end for +#end if +#if $param_out: + -out $param_out +#end if --in ${param_in} --in_seq ${param_in_seq} --out ${param_out} --charge ${param_charge} --format ${param_format} -${param_average_mass} --fragment_type ${param_fragment_type} --separator ${param_separator} --threads \${GALAXY_SLOTS:-24} +#if $rep_param_charge: +-charge + #for token in $rep_param_charge: + #if " " in str(token): + "$token.param_charge" + #else + $token.param_charge + #end if + #end for +#end if +#if $param_format: + -format + #if " " in str($param_format): + "$param_format" + #else + $param_format + #end if +#end if +#if $param_average_mass: + -average_mass +#end if +#if $param_fragment_type: + -fragment_type + #if " " in str($param_fragment_type): + "$param_fragment_type" + #else + $param_fragment_type + #end if +#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_force: + -force +#end if +#end if </command> - <inputs> - <param name="param_in" type="data" format="txt" optional="True" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help="(-in)"/> - <param name="param_in_seq" type="text" size="20" label="List of peptide sequences (mutually exclusive to 'in')" help="(-in_seq)"/> - <param name="param_charge" type="text" size="20" value="0" label="List of charge states; required if 'in_seq' is given" help="(-charge)"/> - <param name="param_format" type="select" optional="True" value="list" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)#br#" help="(-format)"> - <option value="list">list</option> - <option value="table">table</option> - <option value="mass_only">mass_only</option> - <option value="mz_only">mz_only</option> - </param> - <param name="param_average_mass" type="boolean" truevalue="-average_mass true" falsevalue="-average_mass false" checked="false" optional="True" label="Compute average (instead of monoisotopic) peptide masses" help="(-average_mass)"/> - <param name="param_fragment_type" type="select" optional="True" value="full" label="For what type of sequence/fragment the mass should be computed#br#" help="(-fragment_type)"> - <option value="full">full</option> - <option value="internal">internal</option> - <option value="N-terminal">N-terminal</option> - <option value="C-terminal">C-terminal</option> - <option value="a-ion">a-ion</option> - <option value="b-ion">b-ion</option> - <option value="c-ion">c-ion</option> - <option value="x-ion">x-ion</option> - <option value="y-ion">y-ion</option> - <option value="z-ion">z-ion</option> - </param> - <param name="param_separator" type="text" size="20" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="(-separator)"/> - </inputs> - <outputs> - <data name="param_out" label="Output file; if empty, output is written to the screen" format="txt"/> - </outputs> - <help>**What it does** - -Calculates masses and mass-to-charge ratios of peptide sequences + <inputs> + <param format="txt" help="(-in) " label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" name="param_in" optional="True" type="data"/> + <repeat min="0" name="rep_param_in_seq" title="param_in_seq"> + <param help="(-in_seq) " label="List of peptide sequences (mutually exclusive to 'in')" name="param_in_seq" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <repeat max="1" min="0" name="rep_param_charge" title="param_charge"> + <param help="(-charge) " label="List of charge states; required if 'in_seq' is given" name="param_charge" size="30" type="text" value="0"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param help="(-format) " label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" name="param_format" optional="True" type="select" value="list"> + <option value="list">list</option> + <option value="table">table</option> + <option value="mass_only">mass_only</option> + <option value="mz_only">mz_only</option> + </param> + <param checked="false" falsevalue="" help="(-average_mass) " label="Compute average (instead of monoisotopic) peptide masses" name="param_average_mass" optional="True" truevalue="-average_mass" type="boolean"/> + <param help="(-fragment_type) " label="For what type of sequence/fragment the mass should be computed" name="param_fragment_type" optional="True" type="select" value="full"> + <option value="full">full</option> + <option value="internal">internal</option> + <option value="N-terminal">N-terminal</option> + <option value="C-terminal">C-terminal</option> + <option value="a-ion">a-ion</option> + <option value="b-ion">b-ion</option> + <option value="c-ion">c-ion</option> + <option value="x-ion">x-ion</option> + <option value="y-ion">y-ion</option> + <option value="z-ion">z-ion</option> + </param> + <param help="(-separator) " label="Field separator for 'table' output format; by default, the 'tab' character is used" name="param_separator" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <expand macro="advanced_options"> + <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="txt" name="param_out"/> + </outputs> + <help>Calculates masses and mass-to-charge ratios of peptide sequences -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html</help> + </tool>