| Previous changeset 4:7a5ff5359b13 (2022-04-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 |
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modified:
metanovo.xml |
| b |
| diff -r 7a5ff5359b13 -r d6dcd3173bdf metanovo.xml --- a/metanovo.xml Fri Apr 22 13:31:08 2022 +0000 +++ b/metanovo.xml Sat May 11 16:46:46 2024 +0000 |
| [ |
| b'@@ -2,15 +2,18 @@\n <description>\n Produce targeted databases for mass spectrometry analysis.\n </description>\n- <requirements>\n- <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>\n- </requirements>\n <macros>\n <token name="@TOOL_VERSION@">1.9.4</token>\n <token name="@VERSION_SUFFIX@">4</token>\n <token name="@SUBSTITUTION_RX@">[^\\w\\-\\.]</token>\n <import>macros_modifications.xml</import>\n </macros>\n+ <xrefs>\n+ <xref type="bio.tools">metanovo</xref>\n+ </xrefs>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>\n+ </requirements>\n <command>\n <![CDATA[\n #import re\n@@ -152,35 +155,35 @@\n <param name="CHUNKSIZE" label="Size to split fasta for parallel processing" value="100000" type="integer" optional="true"/>\n </section>\n <section name="metanovo_parameters" expanded="False" title="MetaNovo Parameters">\n- <param name="mn_specificity" argument="-mn_specificity" label="Enzyme Specificity" type="select">\n+ <param argument="-mn_specificity" label="Enzyme Specificity" type="select">\n <option selected="true" value="specific">specific</option>\n <option value="semi-specific">semi-specific</option>\n <option value="unspecific">unspecific</option>\n </param>\n- <param name="mn_enzymes" argument="-mn_enzymes" label="Enzyme Rule" type="select">\n+ <param argument="-mn_enzymes" label="Enzyme Rule" type="select">\n <option value="Trypsin">Trypsin</option>\n <option selected="true" value="Trypsin, no P rule">Trypsin, no P rule</option>\n <option value="Whole protein">Whole protein</option>\n </param>\n- <param name="mn_max_missed_cleavages" argument="-mn_max_missed_cleavages" label="Number of enzymatic missed cleavages" value="2" type="integer" optional="true"/>\n+ <param argument="-mn_max_missed_cleavages" label="Number of enzymatic missed cleavages" value="2" type="integer" optional="true"/>\n </section>\n <section name="spectrum_matching_parameters" expanded="False" title="Spectrum Matching Parameters">\n- <param name="prec_tol" argument="-prec_tol" label="Precursor ion mass tolerance" value="10.0" type="float" optional="true"/>\n- <param name="prec_ppm" argument="-prec_ppm" label="Precursor ion tolerance unit" type="select">\n+ <param argument="-prec_tol" label="Precursor ion mass tolerance" value="10.0" type="float" optional="true"/>\n+ <param argument="-prec_ppm" label="Precursor ion tolerance unit" type="select">\n <option value="0">Da</option>\n <option selected="true" value="1">ppm</option>\n </param>\n- <param name="frag_tol" argument="-frag_tol" label="Fragment ion mass tolerance" value="0.05" type="float" optional="true"/>\n- <param name="frag_ppm" argument="-frag_ppm" label="Fragment ion tolerance unit" type="select">\n+ <param argument="-frag_tol" label="Fragment ion mass tolerance" value="0.05" type="float" optional="true"/>\n+ <param argument="-frag_ppm" label="Fragment ion tolerance unit" type="select">\n <option selected="true" value="0">Da</option>\n <option value="1">ppm</option>\n </param>\n- <param name="digestion" argument="-digestion" label="Digestion" type="select">\n+ <param argument="-digestion" label="Digestion" type="select">\n <option selected="true" value="0">Enzyme</option>\n <option value="1">Unspecific</option>\n <option value="2">Whole Protein</option>\n </param>\n- <param name="enzyme" argument="-enzyme" label="Enzyme" type="select" multiple="true">\n+ <param argument="-enzyme" label="Enzyme" type="select" multiple="true">\n <option value="Trypsin">Trypsin</option>\n <option selected="true" value="Trypsin (no P rule)">Trypsin (no P rule)</option>\n <option value="Arg-C">Arg-C</option>\n@@ -199,108 +202,108 @@\n <option value="Thermolysin">Thermolysin</option>'..b' argument="-directag_deisotoping" label="Deisotoping mode" type="select">\n+ <param argument="-directag_tic_cutoff" label="TIC cutoff in percent" value="85" type="integer" optional="true"/>\n+ <param argument="-directag_max_peak_count" label="Max peak count" value="400" type="integer" optional="true"/>\n+ <param argument="-directag_intensity_classes" label="Number of intensity classes" value="3" type="integer" optional="true"/>\n+ <param argument="-directag_adjust_precursor" label="Adjust precursor" truevalue="1" falsevalue="0" type="boolean" checked="false"/>\n+ <param argument="-directag_min_adjustment" label="Minimum precursor adjustment" value="-2.5" type="float" optional="true"/>\n+ <param argument="-directag_max_adjustment" label="Maximum precursor adjustment" value="2.5" type="float" optional="true"/>\n+ <param argument="-directag_adjustment_step" label="Precursor adjustment step" value="0.1" type="float" optional="true"/>\n+ <param argument="-directag_charge_states" label="Number of charge states considered" value="3" type="integer" optional="true"/>\n+ <param argument="-directag_ms_charge_state" label="Use charge state from M spectrum" truevalue="1" falsevalue="0" type="boolean" checked="false"/>\n+ <param argument="-directag_duplicate_spectra" label="Duplicate spectra per charge" truevalue="1" falsevalue="0" type="boolean" checked="true"/>\n+ <param argument="-directag_deisotoping" label="Deisotoping mode" type="select">\n <option selected="true" value="0">No deisotoping</option>\n <option value="1">Precursor only</option>\n <option value="2">Precursor and candidate</option>\n </param>\n- <param name="directag_isotope_tolerance" argument="-directag_isotope_tolerance" label="Isotope mz tolerance" value="0.25" type="float" optional="true"/>\n- <param name="directag_complement_tolerance" argument="-directag_complement_tolerance" label="Complement mz tolerance" value="0.5" type="float" optional="true"/>\n- <param name="directag_tag_length" argument="-directag_tag_length" label="Tag length" value="4" type="integer" optional="true"/>\n- <param name="directag_max_var_mods" argument="-directag_max_var_mods" label="Maximum variable modifications per sequence" value="2" type="integer" optional="true"/>\n- <param name="directag_max_tag_count" argument="-directag_max_tag_count" label="Maximum tag count" value="5" type="integer" optional="true"/>\n- <param name="directag_intensity_weight" argument="-directag_intensity_weight" label="Intensity score weight" value="1.0" type="float" optional="true"/>\n- <param name="directag_fidelity_weight" argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/>\n- <param name="directag_complement_weight" argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/>\n+ <param argument="-directag_isotope_tolerance" label="Isotope mz tolerance" value="0.25" type="float" optional="true"/>\n+ <param argument="-directag_complement_tolerance" label="Complement mz tolerance" value="0.5" type="float" optional="true"/>\n+ <param argument="-directag_tag_length" label="Tag length" value="4" type="integer" optional="true"/>\n+ <param argument="-directag_max_var_mods" label="Maximum variable modifications per sequence" value="2" type="integer" optional="true"/>\n+ <param argument="-directag_max_tag_count" label="Maximum tag count" value="5" type="integer" optional="true"/>\n+ <param argument="-directag_intensity_weight" label="Intensity score weight" value="1.0" type="float" optional="true"/>\n+ <param argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/>\n+ <param argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/>\n </section>\n </inputs>\n <outputs>\n' |