Mercurial > repos > galaxyp > openms_idfilter
comparison IDFilter.xml @ 7:54be6743323c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
| author | galaxyp |
|---|---|
| date | Mon, 12 Feb 2018 12:59:01 -0500 |
| parents | b6ec0f32ad4e |
| children | ce9d29147d5b |
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| 6:382cde407f81 | 7:54be6743323c |
|---|---|
| 1 <?xml version='1.0' encoding='UTF-8'?> | 1 <?xml version='1.0' encoding='UTF-8'?> |
| 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> | 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
| 3 <!--Proposed Tool Section: [ID Processing]--> | 3 <!--Proposed Tool Section: [ID Processing]--> |
| 4 <tool id="IDFilter" name="IDFilter" version="2.2.0"> | 4 <tool id="IDFilter" name="IDFilter" version="2.3.0"> |
| 5 <description>Filters results from protein or peptide identification engines based on different criteria.</description> | 5 <description>Filters results from protein or peptide identification engines based on different criteria.</description> |
| 6 <macros> | 6 <macros> |
| 7 <token name="@EXECUTABLE@">IDFilter</token> | 7 <token name="@EXECUTABLE@">IDFilter</token> |
| 8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
| 9 </macros> | 9 </macros> |
| 223 </sanitizer> | 223 </sanitizer> |
| 224 </param> | 224 </param> |
| 225 <param name="param_score_pep" type="float" value="0.0" label="The score which should be reached by a peptide hit to be kept" help="(-pep) "/> | 225 <param name="param_score_pep" type="float" value="0.0" label="The score which should be reached by a peptide hit to be kept" help="(-pep) "/> |
| 226 <param name="param_score_prot" type="float" value="0.0" label="The score which should be reached by a protein hit to be kept" help="(-prot) Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/> | 226 <param name="param_score_prot" type="float" value="0.0" label="The score which should be reached by a protein hit to be kept" help="(-prot) Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/> |
| 227 <param name="param_whitelist_proteins" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences" help="(-proteins) <br>All peptides that are not referencing a protein in this file are removed. <br>All proteins whose accessions are not present in this file are removed"/> | 227 <param name="param_whitelist_proteins" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences" help="(-proteins) <br>All peptides that are not referencing a protein in this file are removed. <br>All proteins whose accessions are not present in this file are removed"/> |
| 228 <repeat name="rep_param_whitelist_protein_accessions" min="0" max="1" title="param_whitelist_protein_accessions"> | 228 <repeat name="rep_param_whitelist_protein_accessions" min="0" title="param_whitelist_protein_accessions"> |
| 229 <param name="param_whitelist_protein_accessions" type="text" size="30" label="All peptides that do not reference at least one of the provided protein accession are removed" help="(-protein_accessions) <br>Only proteins of the provided list are retained"> | 229 <param name="param_whitelist_protein_accessions" type="text" size="30" label="All peptides that do not reference at least one of the provided protein accession are removed" help="(-protein_accessions) <br>Only proteins of the provided list are retained"> |
| 230 <sanitizer> | 230 <sanitizer> |
| 231 <valid initial="string.printable"> | 231 <valid initial="string.printable"> |
| 232 <remove value="'"/> | 232 <remove value="'"/> |
| 233 <remove value="""/> | 233 <remove value="""/> |
| 235 </sanitizer> | 235 </sanitizer> |
| 236 </param> | 236 </param> |
| 237 </repeat> | 237 </repeat> |
| 238 <param name="param_whitelist_peptides" type="data" format="idxml" optional="True" label="Only peptides with the same sequence and modification assignment as any peptide in this file are kept" help="(-peptides) Use with 'whitelist:ignore_modifications' to only compare by sequence. <br>"/> | 238 <param name="param_whitelist_peptides" type="data" format="idxml" optional="True" label="Only peptides with the same sequence and modification assignment as any peptide in this file are kept" help="(-peptides) Use with 'whitelist:ignore_modifications' to only compare by sequence. <br>"/> |
| 239 <param name="param_whitelist_ignore_modifications" display="radio" type="boolean" truevalue="-whitelist:ignore_modifications" falsevalue="" checked="false" optional="True" label="Compare whitelisted peptides by sequence only" help="(-ignore_modifications) "/> | 239 <param name="param_whitelist_ignore_modifications" display="radio" type="boolean" truevalue="-whitelist:ignore_modifications" falsevalue="" checked="false" optional="True" label="Compare whitelisted peptides by sequence only" help="(-ignore_modifications) "/> |
| 240 <repeat name="rep_param_whitelist_modifications" min="0" max="1" title="param_whitelist_modifications"> | 240 <repeat name="rep_param_whitelist_modifications" min="0" title="param_whitelist_modifications"> |
| 241 <param name="param_whitelist_modifications" type="select" optional="True" label="Keep only peptides with sequences that contain (any of) the selected modification(s)" help="(-modifications) "> | 241 <param name="param_whitelist_modifications" type="select" optional="True" label="Keep only peptides with sequences that contain (any of) the selected modification(s)" help="(-modifications) "> |
| 242 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> | 242 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> |
| 243 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> | 243 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> |
| 244 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> | 244 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> |
| 245 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> | 245 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> |
| 2769 <option value="thioacylPA (K)">thioacylPA (K)</option> | 2769 <option value="thioacylPA (K)">thioacylPA (K)</option> |
| 2770 <option value="trifluoro (L)">trifluoro (L)</option> | 2770 <option value="trifluoro (L)">trifluoro (L)</option> |
| 2771 </param> | 2771 </param> |
| 2772 </repeat> | 2772 </repeat> |
| 2773 <param name="param_blacklist_proteins" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences" help="(-proteins) <br>All peptides that are referencing a protein in this file are removed. <br>All proteins whose accessions are present in this file are removed"/> | 2773 <param name="param_blacklist_proteins" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences" help="(-proteins) <br>All peptides that are referencing a protein in this file are removed. <br>All proteins whose accessions are present in this file are removed"/> |
| 2774 <repeat name="rep_param_blacklist_protein_accessions" min="0" max="1" title="param_blacklist_protein_accessions"> | 2774 <repeat name="rep_param_blacklist_protein_accessions" min="0" title="param_blacklist_protein_accessions"> |
| 2775 <param name="param_blacklist_protein_accessions" type="text" size="30" label="All peptides that reference at least one of the provided protein accession are removed" help="(-protein_accessions) <br>Only proteins not in the provided list are retained"> | 2775 <param name="param_blacklist_protein_accessions" type="text" size="30" label="All peptides that reference at least one of the provided protein accession are removed" help="(-protein_accessions) <br>Only proteins not in the provided list are retained"> |
| 2776 <sanitizer> | 2776 <sanitizer> |
| 2777 <valid initial="string.printable"> | 2777 <valid initial="string.printable"> |
| 2778 <remove value="'"/> | 2778 <remove value="'"/> |
| 2779 <remove value="""/> | 2779 <remove value="""/> |
| 2781 </sanitizer> | 2781 </sanitizer> |
| 2782 </param> | 2782 </param> |
| 2783 </repeat> | 2783 </repeat> |
| 2784 <param name="param_blacklist_peptides" type="data" format="idxml" optional="True" label="Peptides with the same sequence and modification assignment as any peptide in this file are filtered out" help="(-peptides) Use with 'blacklist:ignore_modifications' to only compare by sequence. <br>"/> | 2784 <param name="param_blacklist_peptides" type="data" format="idxml" optional="True" label="Peptides with the same sequence and modification assignment as any peptide in this file are filtered out" help="(-peptides) Use with 'blacklist:ignore_modifications' to only compare by sequence. <br>"/> |
| 2785 <param name="param_blacklist_ignore_modifications" display="radio" type="boolean" truevalue="-blacklist:ignore_modifications" falsevalue="" checked="false" optional="True" label="Compare blacklisted peptides by sequence only" help="(-ignore_modifications) "/> | 2785 <param name="param_blacklist_ignore_modifications" display="radio" type="boolean" truevalue="-blacklist:ignore_modifications" falsevalue="" checked="false" optional="True" label="Compare blacklisted peptides by sequence only" help="(-ignore_modifications) "/> |
| 2786 <repeat name="rep_param_blacklist_modifications" min="0" max="1" title="param_blacklist_modifications"> | 2786 <repeat name="rep_param_blacklist_modifications" min="0" title="param_blacklist_modifications"> |
| 2787 <param name="param_blacklist_modifications" type="select" optional="True" label="Remove all peptides with sequences that contain (any of) the selected modification(s)" help="(-modifications) "> | 2787 <param name="param_blacklist_modifications" type="select" optional="True" label="Remove all peptides with sequences that contain (any of) the selected modification(s)" help="(-modifications) "> |
| 2788 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> | 2788 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> |
| 2789 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> | 2789 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> |
| 2790 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> | 2790 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> |
| 2791 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> | 2791 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> |
| 5316 <option value="trifluoro (L)">trifluoro (L)</option> | 5316 <option value="trifluoro (L)">trifluoro (L)</option> |
| 5317 </param> | 5317 </param> |
| 5318 </repeat> | 5318 </repeat> |
| 5319 <param name="param_digest_fasta" type="data" format="fasta" optional="True" label="Input sequence database in FASTA format" help="(-fasta) "/> | 5319 <param name="param_digest_fasta" type="data" format="fasta" optional="True" label="Input sequence database in FASTA format" help="(-fasta) "/> |
| 5320 <param name="param_digest_enzyme" type="select" optional="False" value="Trypsin" label="Specify the digestion enzyme" help="(-enzyme) "> | 5320 <param name="param_digest_enzyme" type="select" optional="False" value="Trypsin" label="Specify the digestion enzyme" help="(-enzyme) "> |
| 5321 <option value="V8-DE">V8-DE</option> | |
| 5322 <option value="Asp-N_ambic">Asp-N_ambic</option> | |
| 5323 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> | |
| 5324 <option value="Lys-N">Lys-N</option> | |
| 5325 <option value="TrypChymo">TrypChymo</option> | |
| 5326 <option value="leukocyte elastase">leukocyte elastase</option> | |
| 5321 <option value="Formic_acid">Formic_acid</option> | 5327 <option value="Formic_acid">Formic_acid</option> |
| 5328 <option value="Arg-C">Arg-C</option> | |
| 5329 <option value="Trypsin/P">Trypsin/P</option> | |
| 5330 <option value="Trypsin" selected="true">Trypsin</option> | |
| 5331 <option value="proline endopeptidase">proline endopeptidase</option> | |
| 5332 <option value="PepsinA">PepsinA</option> | |
| 5333 <option value="V8-E">V8-E</option> | |
| 5334 <option value="CNBr">CNBr</option> | |
| 5335 <option value="no cleavage">no cleavage</option> | |
| 5336 <option value="Alpha-lytic protease">Alpha-lytic protease</option> | |
| 5322 <option value="unspecific cleavage">unspecific cleavage</option> | 5337 <option value="unspecific cleavage">unspecific cleavage</option> |
| 5323 <option value="V8-DE">V8-DE</option> | 5338 <option value="Chymotrypsin/P">Chymotrypsin/P</option> |
| 5324 <option value="PepsinA">PepsinA</option> | |
| 5325 <option value="Asp-N">Asp-N</option> | 5339 <option value="Asp-N">Asp-N</option> |
| 5326 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> | |
| 5327 <option value="Trypsin/P">Trypsin/P</option> | |
| 5328 <option value="2-iodobenzoate">2-iodobenzoate</option> | 5340 <option value="2-iodobenzoate">2-iodobenzoate</option> |
| 5329 <option value="TrypChymo">TrypChymo</option> | |
| 5330 <option value="Lys-C/P">Lys-C/P</option> | 5341 <option value="Lys-C/P">Lys-C/P</option> |
| 5342 <option value="Asp-N/B">Asp-N/B</option> | |
| 5331 <option value="Lys-C">Lys-C</option> | 5343 <option value="Lys-C">Lys-C</option> |
| 5332 <option value="CNBr">CNBr</option> | |
| 5333 <option value="V8-E">V8-E</option> | |
| 5334 <option value="proline endopeptidase">proline endopeptidase</option> | |
| 5335 <option value="Chymotrypsin">Chymotrypsin</option> | 5344 <option value="Chymotrypsin">Chymotrypsin</option> |
| 5336 <option value="leukocyte elastase">leukocyte elastase</option> | 5345 <option value="Arg-C/P">Arg-C/P</option> |
| 5337 <option value="Asp-N_ambic">Asp-N_ambic</option> | |
| 5338 <option value="no cleavage">no cleavage</option> | |
| 5339 <option value="Trypsin" selected="true">Trypsin</option> | |
| 5340 <option value="Arg-C">Arg-C</option> | |
| 5341 </param> | 5346 </param> |
| 5342 <param name="param_digest_specificity" display="radio" type="select" optional="False" value="full" label="Specificity of the filte" help="(-specificity) "> | 5347 <param name="param_digest_specificity" display="radio" type="select" optional="False" value="full" label="Specificity of the filte" help="(-specificity) "> |
| 5343 <option value="full" selected="true">full</option> | 5348 <option value="full" selected="true">full</option> |
| 5344 <option value="semi">semi</option> | 5349 <option value="semi">semi</option> |
| 5345 <option value="none">none</option> | 5350 <option value="none">none</option> |