Mercurial > repos > galaxyp > openms_peptideindexer
comparison PeptideIndexer.xml @ 10:cb18120926b0 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e9568c650259d95b230d1a243e90f73a19564c2"
| author | galaxyp |
|---|---|
| date | Thu, 24 Sep 2020 09:55:34 +0000 |
| parents | c4a73c6a8dca |
| children | d8ee5700c66b |
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| 9:c4a73c6a8dca | 10:cb18120926b0 |
|---|---|
| 68 <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!"/> | 68 <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!"/> |
| 69 <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"/> | 69 <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"/> |
| 70 <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"/> | 70 <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"/> |
| 71 <section name="enzyme" title="" help="" expanded="false"> | 71 <section name="enzyme" title="" help="" expanded="false"> |
| 72 <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)"> | 72 <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)"> |
| 73 <option value="Chymotrypsin">Chymotrypsin</option> | 73 <option value="Arg-C">Arg-C</option> |
| 74 <option value="Chymotrypsin/P">Chymotrypsin/P</option> | 74 <option value="Arg-C/P">Arg-C/P</option> |
| 75 <option value="CNBr">CNBr</option> | 75 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> |
| 76 <option value="Formic_acid">Formic_acid</option> | 76 <option value="Alpha-lytic protease">Alpha-lytic protease</option> |
| 77 <option value="Asp-N">Asp-N</option> | 77 <option value="Asp-N">Asp-N</option> |
| 78 <option value="Asp-N/B">Asp-N/B</option> | 78 <option value="Asp-N/B">Asp-N/B</option> |
| 79 <option value="Asp-N_ambic">Asp-N_ambic</option> | 79 <option value="Asp-N_ambic">Asp-N_ambic</option> |
| 80 <option value="staphylococcal protease/D">staphylococcal protease/D</option> | |
| 81 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> | |
| 82 <option value="Glu-C+P">Glu-C+P</option> | 80 <option value="Glu-C+P">Glu-C+P</option> |
| 83 <option value="PepsinA + P">PepsinA + P</option> | 81 <option value="PepsinA + P">PepsinA + P</option> |
| 84 <option value="cyanogen-bromide">cyanogen-bromide</option> | 82 <option value="cyanogen-bromide">cyanogen-bromide</option> |
| 85 <option value="Clostripain/P">Clostripain/P</option> | 83 <option value="Clostripain/P">Clostripain/P</option> |
| 86 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> | 84 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> |
| 87 <option value="no cleavage">no cleavage</option> | 85 <option value="no cleavage">no cleavage</option> |
| 88 <option value="unspecific cleavage">unspecific cleavage</option> | 86 <option value="unspecific cleavage">unspecific cleavage</option> |
| 87 <option value="Chymotrypsin">Chymotrypsin</option> | |
| 88 <option value="Chymotrypsin/P">Chymotrypsin/P</option> | |
| 89 <option value="CNBr">CNBr</option> | |
| 90 <option value="Formic_acid">Formic_acid</option> | |
| 91 <option value="Lys-C">Lys-C</option> | |
| 92 <option value="Lys-N">Lys-N</option> | |
| 93 <option value="Lys-C/P">Lys-C/P</option> | |
| 94 <option value="PepsinA">PepsinA</option> | |
| 89 <option value="TrypChymo">TrypChymo</option> | 95 <option value="TrypChymo">TrypChymo</option> |
| 90 <option value="Trypsin/P">Trypsin/P</option> | 96 <option value="Trypsin/P">Trypsin/P</option> |
| 91 <option value="V8-DE">V8-DE</option> | 97 <option value="V8-DE">V8-DE</option> |
| 92 <option value="V8-E">V8-E</option> | 98 <option value="V8-E">V8-E</option> |
| 93 <option value="leukocyte elastase">leukocyte elastase</option> | 99 <option value="leukocyte elastase">leukocyte elastase</option> |
| 94 <option value="proline endopeptidase">proline endopeptidase</option> | 100 <option value="proline endopeptidase">proline endopeptidase</option> |
| 95 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> | |
| 96 <option value="Alpha-lytic protease">Alpha-lytic protease</option> | |
| 97 <option value="2-iodobenzoate">2-iodobenzoate</option> | 101 <option value="2-iodobenzoate">2-iodobenzoate</option> |
| 98 <option value="iodosobenzoate">iodosobenzoate</option> | 102 <option value="iodosobenzoate">iodosobenzoate</option> |
| 99 <option value="Arg-C">Arg-C</option> | 103 <option value="staphylococcal protease/D">staphylococcal protease/D</option> |
| 100 <option value="Arg-C/P">Arg-C/P</option> | 104 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> |
| 101 <option value="Lys-C">Lys-C</option> | |
| 102 <option value="Lys-N">Lys-N</option> | |
| 103 <option value="Lys-C/P">Lys-C/P</option> | |
| 104 <option value="PepsinA">PepsinA</option> | |
| 105 <option value="Trypsin" selected="true">Trypsin</option> | 105 <option value="Trypsin" selected="true">Trypsin</option> |
| 106 <expand macro="list_string_san"/> | 106 <expand macro="list_string_san"/> |
| 107 </param> | 107 </param> |
| 108 <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"> | 108 <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"> |
| 109 <option value="full" selected="true">full</option> | 109 <option value="full" selected="true">full</option> |