Mercurial > repos > galaxyp > openms_peptideindexer

comparison PeptideIndexer.xml @ 11:d8ee5700c66b draft

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"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
comparison
equal deleted inserted replaced
10:cb18120926b0 11:d8ee5700c66b
16 #import re 16 #import re
17 17
18 ## Preprocessing 18 ## Preprocessing
19 mkdir in && 19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir fasta && 21 #if $fasta:
22 ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && 22 mkdir fasta &&
23 ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
24 #end if
23 mkdir out && 25 mkdir out &&
24 26
25 ## Main program call 27 ## Main program call
26 28
27 set -o pipefail && 29 set -o pipefail &&
28 @EXECUTABLE@ -write_ctd ./ && 30 @EXECUTABLE@ -write_ctd ./ &&
29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
31 -in 33 -in
32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 34 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
33 -fasta 35 #if $fasta:
34 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' 36 -fasta
37 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)'
38 #end if
35 -out 39 -out
36 'out/output.${gxy2omsext("idxml")}' 40 'out/output.${gxy2omsext("idxml")}'
37 41
38 ## Postprocessing 42 ## Postprocessing
39 && mv 'out/output.${gxy2omsext("idxml")}' '$out' 43 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
44 <inputs name="args_json" data_style="paths"/> 48 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 50 </configfiles>
47 <inputs> 51 <inputs>
48 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/> 52 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/>
49 <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)"/> 53 <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)"/>
50 <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)"> 54 <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)">
51 <expand macro="list_string_san"/> 55 <expand macro="list_string_san"/>
52 </param> 56 </param>
53 <param name="decoy_string_position" argument="-decoy_string_position" display="radio" type="select" optional="false" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)"> 57 <param name="decoy_string_position" argument="-decoy_string_position" display="radio" type="select" optional="false" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
54 <option value="prefix" selected="true">prefix</option> 58 <option value="prefix" selected="true">prefix</option>
62 <expand macro="list_string_san"/> 66 <expand macro="list_string_san"/>
63 </param> 67 </param>
64 <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=""/> 68 <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=""/>
65 <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=""/> 69 <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=""/>
66 <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=""/> 70 <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=""/>
67 <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"/> 71 <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="">
72 <option value="error" selected="true">error</option>
73 <option value="warn">warn</option>
74 <option value="remove">remove</option>
75 <expand macro="list_string_san"/>
76 </param>
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!"/> 77 <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"/> 78 <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"/> 79 <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"> 80 <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)"> 81 <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">
82 <option value="auto" selected="true">auto</option>
83 <option value="Asp-N/B">Asp-N/B</option>
84 <option value="Asp-N_ambic">Asp-N_ambic</option>
85 <option value="Chymotrypsin">Chymotrypsin</option>
86 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
87 <option value="CNBr">CNBr</option>
88 <option value="proline endopeptidase">proline endopeptidase</option>
89 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
90 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
91 <option value="2-iodobenzoate">2-iodobenzoate</option>
92 <option value="iodosobenzoate">iodosobenzoate</option>
93 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
94 <option value="PepsinA">PepsinA</option>
95 <option value="TrypChymo">TrypChymo</option>
96 <option value="Trypsin/P">Trypsin/P</option>
97 <option value="V8-DE">V8-DE</option>
98 <option value="V8-E">V8-E</option>
99 <option value="leukocyte elastase">leukocyte elastase</option>
73 <option value="Arg-C">Arg-C</option> 100 <option value="Arg-C">Arg-C</option>
74 <option value="Arg-C/P">Arg-C/P</option> 101 <option value="Arg-C/P">Arg-C/P</option>
75 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
76 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
77 <option value="Asp-N">Asp-N</option> 102 <option value="Asp-N">Asp-N</option>
78 <option value="Asp-N/B">Asp-N/B</option> 103 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
79 <option value="Asp-N_ambic">Asp-N_ambic</option>
80 <option value="Glu-C+P">Glu-C+P</option> 104 <option value="Glu-C+P">Glu-C+P</option>
81 <option value="PepsinA + P">PepsinA + P</option> 105 <option value="PepsinA + P">PepsinA + P</option>
82 <option value="cyanogen-bromide">cyanogen-bromide</option> 106 <option value="cyanogen-bromide">cyanogen-bromide</option>
83 <option value="Clostripain/P">Clostripain/P</option> 107 <option value="Clostripain/P">Clostripain/P</option>
84 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> 108 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
85 <option value="no cleavage">no cleavage</option> 109 <option value="no cleavage">no cleavage</option>
86 <option value="unspecific cleavage">unspecific cleavage</option> 110 <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> 111 <option value="Formic_acid">Formic_acid</option>
91 <option value="Lys-C">Lys-C</option> 112 <option value="Lys-C">Lys-C</option>
92 <option value="Lys-N">Lys-N</option> 113 <option value="Lys-N">Lys-N</option>
93 <option value="Lys-C/P">Lys-C/P</option> 114 <option value="Lys-C/P">Lys-C/P</option>
94 <option value="PepsinA">PepsinA</option> 115 <option value="Trypsin">Trypsin</option>
95 <option value="TrypChymo">TrypChymo</option>
96 <option value="Trypsin/P">Trypsin/P</option>
97 <option value="V8-DE">V8-DE</option>
98 <option value="V8-E">V8-E</option>
99 <option value="leukocyte elastase">leukocyte elastase</option>
100 <option value="proline endopeptidase">proline endopeptidase</option>
101 <option value="2-iodobenzoate">2-iodobenzoate</option>
102 <option value="iodosobenzoate">iodosobenzoate</option>
103 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
104 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
105 <option value="Trypsin" selected="true">Trypsin</option>
106 <expand macro="list_string_san"/> 116 <expand macro="list_string_san"/>
107 </param> 117 </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"> 118 <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)">
109 <option value="full" selected="true">full</option> 119 <option value="auto" selected="true">auto</option>
120 <option value="full">full</option>
110 <option value="semi">semi</option> 121 <option value="semi">semi</option>
111 <option value="none">none</option> 122 <option value="none">none</option>
112 <expand macro="list_string_san"/> 123 <expand macro="list_string_san"/>
113 </param> 124 </param>
114 </section> 125 </section>
115 <expand macro="adv_opts_macro"> 126 <expand macro="adv_opts_macro">
116 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 127 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
117 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 128 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
118 <expand macro="list_string_san"/> 129 <expand macro="list_string_san"/>
119 </param> 130 </param>
120 </expand> 131 </expand>
121 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 132 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
122 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 133 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
123 </param> 134 </param>
124 </inputs> 135 </inputs>
125 <outputs> 136 <outputs>
126 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 137 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
133 <expand macro="manutest_PeptideIndexer"/> 144 <expand macro="manutest_PeptideIndexer"/>
134 </tests> 145 </tests>
135 <help><![CDATA[Refreshes the protein references for all peptide hits. 146 <help><![CDATA[Refreshes the protein references for all peptide hits.
136 147
137 148
138 For more information, visit http://www.openms.de/documentation/TOPP_PeptideIndexer.html]]></help> 149 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PeptideIndexer.html]]></help>
139 <expand macro="references"/> 150 <expand macro="references"/>
140 </tool> 151 </tool>