Mercurial > repos > galaxyp > unipept

comparison unipept.xml @ 3:34758ab8aaa4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author galaxyp
date Mon, 20 Feb 2017 10:32:03 -0500
parents 503ab8a39006
children 4953dcd7dd39
comparison
equal deleted inserted replaced
2:503ab8a39006 3:34758ab8aaa4
1 <tool id="unipept" name="Unipept" version="1.1.0"> 1 <tool id="unipept" name="Unipept" version="2.0.1">
2 <description>retrieve taxonomy for peptides</description> 2 <description>retrieve taxonomy for peptides</description>
3 <macros> 3 <macros>
4 <xml name="equate_il"> 4 <xml name="equate_il">
5 <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine"> 5 <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine">
6 <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help> 6 <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help>
7 </param > 7 </param>
8 </xml> 8 </xml>
9 <xml name="extra"> 9 <xml name="extra">
10 <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="false" label="retrieve extra information"> 10 <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="false" label="retrieve extra information">
11 <yield/> 11 <yield/>
12 </param > 12 </param>
13 </xml>
14 <xml name="extra_true">
15 <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="true" label="retrieve extra information">
16 <yield/>
17 </param>
13 </xml> 18 </xml>
14 <xml name="names"> 19 <xml name="names">
15 <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" > 20 <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" >
16 <help>return the names in complete taxonomic lineage</help> 21 <help>return the names in complete taxonomic lineage</help>
17 </param > 22 </param>
18 <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" > 23 <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" >
19 <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help> 24 <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help>
20 </param > 25 </param>
21 </xml> 26 </xml>
22 </macros> 27 </macros>
23 <requirements> 28 <requirements>
24 <requirement type="package" version="2.7.12">python</requirement> 29 <requirement type="package" version="2.7">python</requirement>
25 </requirements> 30 </requirements>
26 <stdio> 31 <stdio>
27 <exit_code range="1:" /> 32 <exit_code range="1:" />
28 </stdio> 33 </stdio>
29 <command interpreter="python"><![CDATA[ 34 <command><![CDATA[
30 unipept.py 35 python '$__tool_directory__/unipept.py'
31 --api=$unipept.api 36 --api=$unipept.api
32 $unipept.equate_il $unipept.extra 37 $unipept.equate_il $unipept.extra
33 #if $unipept.api != 'pept2prot': 38 #if $unipept.api != 'pept2prot':
34 $unipept.names $unipept.allfields 39 $unipept.names $unipept.allfields
35 #end if 40 #end if
51 #elif str($peptide_src.fmt) == 'mzid': 56 #elif str($peptide_src.fmt) == 'mzid':
52 --mzid="$peptide_src.input_mzid" 57 --mzid="$peptide_src.input_mzid"
53 #elif str($peptide_src.fmt) == 'pepxml': 58 #elif str($peptide_src.fmt) == 'pepxml':
54 --pepxml="$peptide_src.input_pepxml" 59 --pepxml="$peptide_src.input_pepxml"
55 #end if 60 #end if
56 #if 'json' in str($outputs).split(','): 61 #if 'json' in str($outputs).split(',') and str($unipept.api) != 'pept2prot':
57 --json $output_json 62 --json $output_json
58 #end if 63 #end if
59 #if 'tsv' in str($outputs).split(','): 64 #if 'tsv' in str($outputs).split(','):
60 --tsv $output_tsv 65 --tsv $output_tsv
61 #end if 66 #end if
80 </expand> 85 </expand>
81 <expand macro="names" /> 86 <expand macro="names" />
82 </when> 87 </when>
83 <when value="pept2taxa"> 88 <when value="pept2taxa">
84 <expand macro="equate_il" /> 89 <expand macro="equate_il" />
85 <expand macro="extra"> 90 <expand macro="extra_true">
86 <checked>true</checked>
87 <help>Return the complete lineage of each organism, and include ID fields.</help> 91 <help>Return the complete lineage of each organism, and include ID fields.</help>
88 </expand> 92 </expand>
89 <expand macro="names" /> 93 <expand macro="names" />
90 </when> 94 </when>
91 <when value="pept2prot"> 95 <when value="pept2prot">
123 </when> 127 </when>
124 </conditional> 128 </conditional>
125 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> 129 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
126 <option value="tsv" selected="true">tabular</option> 130 <option value="tsv" selected="true">tabular</option>
127 <option value="csv">Comma Separated Values (.csv)</option> 131 <option value="csv">Comma Separated Values (.csv)</option>
128 <option value="json">JSON</option> 132 <option value="json">JSON Taxomony Tree (ignored for pept2prot)</option>
129 <option value="unmatched">Unmatched peptides</option> 133 <option value="unmatched">Unmatched peptides</option>
130 </param> 134 </param>
131 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/> 135 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
132 </inputs> 136 </inputs>
133 <outputs> 137 <outputs>
134 <data name="output_json" format="json" label="${tool.name} ${unipept.api} on ${on_string} json"> 138 <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} json">
135 <filter>'json' in outputs</filter> 139 <filter>'json' in outputs and unipept['api'] != 'pept2prot'</filter>
140 <change_format>
141 <when input="api" value="pept2prot" format="json" />
142 </change_format>
136 </data> 143 </data>
137 <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv"> 144 <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv">
138 <filter>'tsv' in outputs</filter> 145 <filter>'tsv' in outputs</filter>
139 </data> 146 </data>
140 <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv"> 147 <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv">