Mercurial > repos > galaxyp > openms_peptideindexer
diff PeptideIndexer.xml @ 11:d8ee5700c66b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 20:36:24 +0000 |
| parents | cb18120926b0 |
| children | d6aca689dd48 |
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--- a/PeptideIndexer.xml Thu Sep 24 09:55:34 2020 +0000 +++ b/PeptideIndexer.xml Tue Oct 13 20:36:24 2020 +0000 @@ -18,8 +18,10 @@ ## Preprocessing mkdir in && ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && -mkdir fasta && -ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && +#if $fasta: + mkdir fasta && + ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && +#end if mkdir out && ## Main program call @@ -30,8 +32,10 @@ @EXECUTABLE@ -ini @EXECUTABLE@.ctd -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' --fasta -'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' +#if $fasta: + -fasta + 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' +#end if -out 'out/output.${gxy2omsext("idxml")}' @@ -46,7 +50,7 @@ </configfiles> <inputs> <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/> - <param name="fasta" argument="-fasta" type="data" format="fasta" optional="false" label="Input sequence database in FASTA format" help="Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/> + <param name="fasta" argument="-fasta" type="data" format="fasta" optional="true" label="Input sequence database in FASTA format" help="Leave empty for using the same DB as used for the input idXML (this might fail). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/> <param name="decoy_string" argument="-decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)"> <expand macro="list_string_san"/> </param> @@ -64,19 +68,39 @@ <param name="write_protein_sequence" argument="-write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/> <param name="write_protein_description" argument="-write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/> <param name="keep_unreferenced_proteins" argument="-keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/> - <param name="allow_unmatched" argument="-allow_unmatched" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, unmatched peptide sequences are allowed" help="By default (i.e. if this flag is not set) the program terminates with an error on unmatched peptides"/> + <param name="unmatched_action" argument="-unmatched_action" display="radio" type="select" optional="false" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help=""> + <option value="error" selected="true">error</option> + <option value="warn">warn</option> + <option value="remove">remove</option> + <expand macro="list_string_san"/> + </param> <param name="aaa_max" argument="-aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are B, J, Z and X!"/> <param name="mismatches_max" argument="-mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/> <param name="IL_equivalent" argument="-IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/> <section name="enzyme" title="" help="" expanded="false"> - <param name="name" argument="-enzyme:name" type="select" optional="false" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)"> + <param name="name" argument="-enzyme:name" type="select" optional="false" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input"> + <option value="auto" selected="true">auto</option> + <option value="Asp-N/B">Asp-N/B</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Chymotrypsin/P">Chymotrypsin/P</option> + <option value="CNBr">CNBr</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="Alpha-lytic protease">Alpha-lytic protease</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="iodosobenzoate">iodosobenzoate</option> + <option value="staphylococcal protease/D">staphylococcal protease/D</option> + <option value="PepsinA">PepsinA</option> + <option value="TrypChymo">TrypChymo</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="V8-DE">V8-DE</option> + <option value="V8-E">V8-E</option> + <option value="leukocyte elastase">leukocyte elastase</option> <option value="Arg-C">Arg-C</option> <option value="Arg-C/P">Arg-C/P</option> - <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <option value="Alpha-lytic protease">Alpha-lytic protease</option> <option value="Asp-N">Asp-N</option> - <option value="Asp-N/B">Asp-N/B</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> <option value="Glu-C+P">Glu-C+P</option> <option value="PepsinA + P">PepsinA + P</option> <option value="cyanogen-bromide">cyanogen-bromide</option> @@ -84,41 +108,28 @@ <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> <option value="no cleavage">no cleavage</option> <option value="unspecific cleavage">unspecific cleavage</option> - <option value="Chymotrypsin">Chymotrypsin</option> - <option value="Chymotrypsin/P">Chymotrypsin/P</option> - <option value="CNBr">CNBr</option> <option value="Formic_acid">Formic_acid</option> <option value="Lys-C">Lys-C</option> <option value="Lys-N">Lys-N</option> <option value="Lys-C/P">Lys-C/P</option> - <option value="PepsinA">PepsinA</option> - <option value="TrypChymo">TrypChymo</option> - <option value="Trypsin/P">Trypsin/P</option> - <option value="V8-DE">V8-DE</option> - <option value="V8-E">V8-E</option> - <option value="leukocyte elastase">leukocyte elastase</option> - <option value="proline endopeptidase">proline endopeptidase</option> - <option value="2-iodobenzoate">2-iodobenzoate</option> - <option value="iodosobenzoate">iodosobenzoate</option> - <option value="staphylococcal protease/D">staphylococcal protease/D</option> - <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> - <option value="Trypsin" selected="true">Trypsin</option> + <option value="Trypsin">Trypsin</option> <expand macro="list_string_san"/> </param> - <param name="specificity" argument="-enzyme:specificity" display="radio" type="select" optional="false" label="Specificity of the enzyme" help="'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here"> - <option value="full" selected="true">full</option> + <param name="specificity" argument="-enzyme:specificity" display="radio" type="select" optional="false" label="Specificity of the enzyme" help="Default: deduce from input.. 'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context (enzyme is irrelevant)"> + <option value="auto" selected="true">auto</option> + <option value="full">full</option> <option value="semi">semi</option> <option value="none">none</option> <expand macro="list_string_san"/> </param> </section> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> <expand macro="list_string_san"/> </param> </expand> - <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> @@ -135,6 +146,6 @@ <help><![CDATA[Refreshes the protein references for all peptide hits. -For more information, visit http://www.openms.de/documentation/TOPP_PeptideIndexer.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PeptideIndexer.html]]></help> <expand macro="references"/> </tool>