Mercurial > repos > bgruening > openms
diff Digestor.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/Digestor.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/Digestor.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,51 +1,95 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="Digestor" name="Digestor" version="1.12.0"> - <description>Digests a protein database in-silico.</description> - <macros> - <token name="@EXECUTABLE@">Digestor</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>Digestor +<?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="Digestor" name="Digestor" version="2.0.0"> + <description>Digests a protein database in-silico.</description> + <macros> + <token name="@EXECUTABLE@">Digestor</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>Digestor --in ${param_in} --out ${param_out} --out_type ${param_out_type} --missed_cleavages ${param_missed_cleavages} --min_length ${param_min_length} --max_length ${param_max_length} --enzyme ${param_enzyme} --threads \${GALAXY_SLOTS:-24} +#if $param_in: + -in $param_in +#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_missed_cleavages: + -missed_cleavages $param_missed_cleavages +#end if +#if $param_min_length: + -min_length $param_min_length +#end if +#if $param_max_length: + -max_length $param_max_length +#end if +#if $param_enzyme: + -enzyme + #if " " in str($param_enzyme): + "$param_enzyme" + #else + $param_enzyme + #end if +#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="fasta" optional="False" label="input file" help="(-in)"/> - <param name="param_out_type" type="select" optional="True" label="Set this if you cannot control the filename of 'out', e.g., in TOPPAS." help="(-out_type)"> - <option value="idXML">idXML</option> - <option value="fasta">fasta</option> - </param> - <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="The number of allowed missed cleavages" help="(-missed_cleavages)"/> - <param name="param_min_length" type="integer" value="6" label="Minimum length of peptide" help="(-min_length)"/> - <param name="param_max_length" type="integer" value="40" label="Maximum length of peptide" help="(-max_length)"/> - <param name="param_enzyme" type="select" optional="True" value="Trypsin" label="The type of digestion enzyme" help="(-enzyme)"> - <option value="Trypsin">Trypsin</option> - <option value="none">none</option> - </param> - </inputs> - <outputs> - <data name="param_out" label="Output file (peptides)" format="fasta"> - <change_format> - <when input="param_out_type" value="idXML" format="idXML"/> - </change_format> - </data> - </outputs> - <help>**What it does** - -Digests a protein database in-silico. + <inputs> + <param format="fasta" help="(-in) " label="input file" name="param_in" optional="False" type="data"/> + <param help="(-out_type) e.g., in TOPPAS" label="Set this if you cannot control the filename of 'out'," name="param_out_type" optional="True" type="select"> + <option value="idXML">idXML</option> + <option value="fasta">fasta</option> + </param> + <param help="(-missed_cleavages) " label="The number of allowed missed cleavages" min="0" name="param_missed_cleavages" optional="True" type="integer" value="1"/> + <param help="(-min_length) " label="Minimum length of peptide" name="param_min_length" type="integer" value="6"/> + <param help="(-max_length) " label="Maximum length of peptide" name="param_max_length" type="integer" value="40"/> + <param help="(-enzyme) " label="The type of digestion enzyme" name="param_enzyme" optional="True" type="select" value="Trypsin"> + <option value="no cleavage">no cleavage</option> + <option value="Arg-C">Arg-C</option> + <option value="Lys-C">Lys-C</option> + <option value="PepsinA">PepsinA</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="unspecific cleavage">unspecific cleavage</option> + <option value="V8-DE">V8-DE</option> + <option value="CNBr">CNBr</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="Formic_acid">Formic_acid</option> + <option value="TrypChymo">TrypChymo</option> + <option value="Asp-N">Asp-N</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="V8-E">V8-E</option> + <option value="Trypsin">Trypsin</option> + </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="xml" name="param_out"/> + </outputs> + <help>Digests a protein database in-silico. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html</help> + </tool>