Mercurial > repos > proteore > proteore_id_converter

comparison id_converter.xml @ 49:ab8ea848cc00 draft default tip

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"planemo upload commit df0bcf958cf0b89a682b764b53f50950b9ed79b6-dirty"
author proteore
date Tue, 08 Jun 2021 14:25:34 +0000
parents 135ef5524bfc
children
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48:135ef5524bfc 49:ab8ea848cc00
1 <tool id="IDconverter" name="ID Converter" version="2020.01.09"> 1 <tool id="idconverter" name="id converter" version="2021.06.03">
2 <description>(Human, Mouse, Rat) 2 <description>(Human, Mouse, Rat)
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 </requirements> 5 </requirements>
6 <stdio> 6 <command detect_errors="aggressive"><![CDATA[
7 <exit_code range="1:" /> 7 python '$__tool_directory__/id_converter.py'
8 </stdio> 8 --id_type='$species.idtypein'
9 <command><![CDATA[ 9 #if $input.ids == 'text'
10 python $__tool_directory__/id_converter.py 10 --input='$input.txt'
11 --id_type="$species.idtypein" 11 --input_type='list'
12 #if $input.ids == "text"
13 --input="$input.txt"
14 --input_type="list"
15 #else 12 #else
16 --input="$input.file" 13 --input='$input.file'
17 --column_number="$input.ncol" 14 --column_number='$input.ncol'
18 --header="$input.header" 15 --header='$input.header'
19 --input_type="file" 16 --input_type='file'
20 #end if 17 #end if
21 --target_ids="$species.idto.idtypeout" 18 --target_ids='$species.idto.idtypeout'
22 --output="$output" 19 --output='$output'
23 #if "id_mapping" in str($species.mapping_file).split("/") 20 #if 'id_mapping' in str($species.mapping_file).split("/")
24 --ref_file="$species.mapping_file" 21 --ref_file='$species.mapping_file'
25 #else 22 #else
26 --ref_file="$__tool_directory__/$species.mapping_file" 23 --ref_file='$__tool_directory__/$species.mapping_file'
27 #end if 24 #end if
28 ]]></command> 25 ]]></command>
29 <inputs> 26 <inputs>
30 <conditional name="input" > 27 <conditional name="input" >
31 <param name="ids" type="select" label="Enter IDs" help="Copy/paste or from a file (e.g. table)" > 28 <param name="ids" type="select" label="Enter IDs" help="Copy/paste or from a file (e.g. table)" >
214 </outputs> 211 </outputs>
215 <tests> 212 <tests>
216 <test> 213 <test>
217 <conditional name="input" > 214 <conditional name="input" >
218 <param name="ids" value="file"/> 215 <param name="ids" value="file"/>
219 <param name="file" value="FKW_Lacombe_et_al_2017_OK.txt" /> 216 <param name="file" value='FKW_Lacombe_et_al_2017_OK.txt' />
220 <param name="header" value="true" /> 217 <param name="header" value="true" />
221 <param name="ncol" value="c1"/> 218 <param name="ncol" value="c1"/>
222 </conditional> 219 </conditional>
223 <conditional name="species"> 220 <conditional name="species">
224 <param name="mapping_file" value="human_id_mapping"/> 221 <param name="mapping_file" value='human_id_mapping_file.tsv'/>
225 <param name="idtypein" value="UniProt-AC"/> 222 <param name="idtypein" value="UniProt-AC"/>
226 <section name="idto"> 223 <section name="idto">
227 <param name="idtypeout" value="neXtProt,UniProt-ID,GeneID,MIM,Ensembl_Gene" /> 224 <param name="idtypeout" value="neXtProt,UniProt-ID,GeneID,MIM,Ensembl_Gene" />
228 </section> 225 </section>
229 </conditional> 226 </conditional>