Mercurial > repos > galaxyp > openms_rnpxl
view RNPxl.xml @ 8:4dbfc881d14f draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty
| author | galaxyp |
|---|---|
| date | Fri, 17 May 2019 09:26:40 -0400 |
| parents | 49d8333edbfb |
| children |
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<?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: [Utilities]--> <tool id="RNPxl" name="RNPxl" version="2.3.0"> <description>Tool for RNP cross linking experiment analysis.</description> <macros> <token name="@EXECUTABLE@">RNPxl</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[RNPxl #if $param_in_mzML: -in_mzML $param_in_mzML #end if #if $param_length: -length $param_length #end if #if $param_sequence: -sequence "$param_sequence" #end if #if $rep_param_target_nucleotides: -target_nucleotides #for token in $rep_param_target_nucleotides: #if " " in str(token): "$token.param_target_nucleotides" #else $token.param_target_nucleotides #end if #end for #end if #if $rep_param_mapping: -mapping #for token in $rep_param_mapping: #if " " in str(token): "$token.param_mapping" #else $token.param_mapping #end if #end for #end if #if $rep_param_restrictions: -restrictions #for token in $rep_param_restrictions: #if " " in str(token): "$token.param_restrictions" #else $token.param_restrictions #end if #end for #end if #if $rep_param_modifications: -modifications #for token in $rep_param_modifications: #if " " in str(token): "$token.param_modifications" #else $token.param_modifications #end if #end for #end if #if $param_peptide_mass_threshold: -peptide_mass_threshold $param_peptide_mass_threshold #end if #if $param_precursor_variant_mz_threshold: -precursor_variant_mz_threshold $param_precursor_variant_mz_threshold #end if #if $param_CysteineAdduct: -CysteineAdduct #end if #if $param_in_OMSSA_ini: -in_OMSSA_ini $param_in_OMSSA_ini #end if #if $param_in_fasta: -in_fasta $param_in_fasta #end if #if $param_marker_ions_tolerance: -marker_ions_tolerance $param_marker_ions_tolerance #end if #if $param_out_idXML: -out_idXML $param_out_idXML #end if #if $param_out_csv: -out_csv $param_out_csv #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_continue: -continue #end if #if $adv_opts.param_force: -force #end if #end if ]]></command> <inputs> <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Input file" help="(-in_mzML) "/> <param name="param_length" type="integer" value="4" label="Oligonucleotide maximum length" help="(-length) "/> <param name="param_sequence" type="text" size="30" label="Sequence to restrict the generation of oligonucleotide chains" help="(-sequence) (disabled for empty sequence)"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <repeat name="rep_param_target_nucleotides" min="0" max="1" title="param_target_nucleotides"> <param name="param_target_nucleotides" type="text" size="30" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format: target nucleotide=empirical formula of nucleoside monophosphate" help="(-target_nucleotides) e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU <br> or e.g. Y=C10H14N5O7PS where Y represents tG"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <repeat name="rep_param_mapping" min="0" max="1" title="param_mapping"> <param name="param_mapping" type="text" size="30" value="A->A C->C G->G U->U" label="format: source->target e.g. A->A, ..., U->U, U->X" help="(-mapping) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <repeat name="rep_param_restrictions" min="0" max="1" title="param_restrictions"> <param name="param_restrictions" type="text" size="30" value="A=0 C=0 U=0 G=0" label="format: target nucleotide=min_count: e.g U=1 if at least one U must be in the generated sequence" help="(-restrictions) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <repeat name="rep_param_modifications" min="0" max="1" title="param_modifications"> <param name="param_modifications" type="text" size="30" value="-H2O -H2O-HPO3 -HPO3 -H2O+HPO3 +HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help="(-modifications) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <param name="param_peptide_mass_threshold" type="float" value="600.0" label="Lower peptide mass (Da) threshold" help="(-peptide_mass_threshold) "/> <param name="param_precursor_variant_mz_threshold" type="float" value="260.0" label="Lower m/z (Th) threshold for precursor variant" help="(-precursor_variant_mz_threshold) "/> <param name="param_CysteineAdduct" display="radio" type="boolean" truevalue="-CysteineAdduct" falsevalue="" checked="false" optional="True" label="Use this flag if the +152 adduct is expected" help="(-CysteineAdduct) "/> <param name="param_in_OMSSA_ini" type="data" format="txt" optional="False" label="Ini file for the OMSSA search engine" help="(-in_OMSSA_ini) "/> <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Fasta file for search result annotation" help="(-in_fasta) "/> <param name="param_marker_ions_tolerance" type="float" value="0.05" label="mz tolerance used to determine marker ions" help="(-marker_ions_tolerance) "/> <expand macro="advanced_options"> <param name="param_continue" display="radio" type="boolean" truevalue="-continue" falsevalue="" checked="false" optional="True" label="Do not recreate intermediate files to continue after unexpected crash" help="(-continue) "/> <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> </expand> </inputs> <outputs> <data name="param_out_idXML" format="idxml"/> <data name="param_out_csv" format="tabular"/> </outputs> <help>Tool for RNP cross linking experiment analysis. For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_RNPxl.html</help> </tool>