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comparison IDFilter.xml @ 7:54be6743323c draft

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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
comparison
equal deleted inserted replaced
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) &lt;br&gt;All peptides that are not referencing a protein in this file are removed. &lt;br&gt;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) &lt;br&gt;All peptides that are not referencing a protein in this file are removed. &lt;br&gt;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) &lt;br&gt;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) &lt;br&gt;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="&quot;"/> 233 <remove value="&quot;"/>
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. &lt;br&gt;"/> 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. &lt;br&gt;"/>
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) &lt;br&gt;All peptides that are referencing a protein in this file are removed. &lt;br&gt;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) &lt;br&gt;All peptides that are referencing a protein in this file are removed. &lt;br&gt;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) &lt;br&gt;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) &lt;br&gt;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="&quot;"/> 2779 <remove value="&quot;"/>
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. &lt;br&gt;"/> 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. &lt;br&gt;"/>
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>