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<?xml version='1.0' encoding='UTF-8'?>
<tool id="RNPxl" name="RNPxl" version="1.12.0">
  <description>Tool for RNP cross linking experiment analysis.</description>
  <macros>
    <token name="@EXECUTABLE@">RNPxl</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>RNPxl

-in_mzML ${param_in_mzML}
-length ${param_length}
-sequence ${param_sequence}
-target_nucleotides ${param_target_nucleotides}
-mapping ${param_mapping}
-restrictions ${param_restrictions}
-modifications ${param_modifications}
-peptide_mass_threshold ${param_peptide_mass_threshold}
-precursor_variant_mz_threshold ${param_precursor_variant_mz_threshold}
${param_CysteineAdduct}
-in_OMSSA_ini ${param_in_OMSSA_ini}
-in_fasta ${param_in_fasta}
-marker_ions_tolerance ${param_marker_ions_tolerance}
-out_idXML ${param_out_idXML}
-out_csv ${param_out_csv}
-threads \${GALAXY_SLOTS:-24} 
</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="20" label="Sequence to restrict the generation of oligonucleotide chains. (disabled for empty sequence)" help="(-sequence)"/>
    <param name="param_target_nucleotides" type="text" size="20" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format:  target nucleotide=empirical formula of nucleoside monophosphate #br# e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS  where X represents e.g. tU #br# or e.g. Y=C10H14N5O7PS where Y represents tG" help="(-target_nucleotides)"/>
    <param name="param_mapping" type="text" size="20" value="A-&gt;A C-&gt;C G-&gt;G U-&gt;U" label="format: source-&gt;target e.g. A-&gt;A, ..., U-&gt;U, U-&gt;X" help="(-mapping)"/>
    <param name="param_restrictions" type="text" size="20" 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)"/>
    <param name="param_modifications" type="text" size="20" value="-H2O  -H2O-HPO3 -HPO3 -H2O+HPO3 +HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help="(-modifications)"/>
    <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" type="boolean" truevalue="-CysteineAdduct true" falsevalue="-CysteineAdduct false" 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="" optional="False" label="Ini file for the OMSSA search engine#br#" help="(-in_OMSSA_ini)"/>
    <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Fasta file for search result annotation#br#" 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)"/>
  </inputs>
  <outputs>
    <data name="param_out_idXML" label="idXML output file#br#" format="idXML"/>
    <data name="param_out_csv" label="csv output file#br#" format="tabular"/>
  </outputs>
  <help>**What it does**

Tool for RNP cross linking experiment analysis.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxl.html

@REFERENCES@
</help>
</tool>