Mercurial > repos > galaxyp > metanovo

comparison metanovo.xml @ 3:4a851c02f558 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 420ef6b0ee91e44ed354366a55575c1aa504e380"
author galaxyp
date Tue, 29 Mar 2022 20:53:42 +0000
parents 08b5b0977c61
children 7a5ff5359b13
comparison
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2:08b5b0977c61 3:4a851c02f558
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>
7 </requirements> 7 </requirements>
8 <macros> 8 <macros>
9 <token name="@TOOL_VERSION@">1.9.4</token> 9 <token name="@TOOL_VERSION@">1.9.4</token>
10 <token name="@VERSION_SUFFIX@">2</token> 10 <token name="@VERSION_SUFFIX@">3</token>
11 <token name="@SUBSTITUTION_RX@">[^\w\-\.]</token> 11 <token name="@SUBSTITUTION_RX@">[^\w\-\.]</token>
12 <import>macros_modifications.xml</import> 12 <import>macros_modifications.xml</import>
13 </macros> 13 </macros>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
20 mkdir $mgf_dir && 20 mkdir $mgf_dir &&
21 mkdir $fasta_dir && 21 mkdir $fasta_dir &&
22 ln -s '$input_fasta' '$fasta_dir/$fasta_name' && 22 ln -s '$input_fasta' '$fasta_dir/$fasta_name' &&
23 23
24 #if $input_type.type == "collection" 24 #if $input_type.type == "collection"
25 #set mgf_names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $input_type.input_mgf_collection] 25 #for $input_mgf_item in $input_type.input_mgf_collection:
26 #for $mgf_name in $mgf_names: 26 #set mgf_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_mgf_item.element_identifier))
27 ln -s '$input' '$mgf_dir/$mgf_name' && 27 ln -s '$input_mgf_item' '$mgf_dir/$mgf_name' &&
28 #end for 28 #end for
29 #else 29 #else
30 #set mgf_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_type.input_mgf.element_identifier)) 30 #set mgf_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_type.input_mgf.element_identifier))
31 ln -s '$input_mgf' '$mgf_dir/$mgf_name' && 31 ln -s '$input_type.input_mgf' '$mgf_dir/$mgf_name' &&
32 #end if 32 #end if
33 33
34 cat $metanovo_config > config.sh && 34 cat $metanovo_config > config.sh &&
35 metanovo.sh config.sh 35 metanovo.sh config.sh
36 ]]> 36 ]]>