Mercurial > repos > galaxyp > openms_rnpxl
diff RNPxl.xml @ 0:43ddae9b94a4 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:42:27 -0500 |
| parents | |
| children | 3aa12d9ec7ee |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/RNPxl.xml Wed Mar 01 12:42:27 2017 -0500 @@ -0,0 +1,171 @@ +<?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="RNPxl" name="RNPxl" version="2.1.0"> + <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>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 http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxl.html</help> +</tool>