Mercurial > repos > iuc > nanocompore_sampcomp

comparison sampcomp.xml @ 4:89b4ed4145b3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 51078f4c0eab9cc41a0cb2190000e428322631a4
author iuc
date Thu, 23 Jun 2022 17:27:25 +0000
parents e7d7d87dc1a3
children
comparison
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3:e7d7d87dc1a3 4:89b4ed4145b3
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="nanocompore_sampcomp" name="SampComp" version="@TOOL_VERSION@+galaxy0"> 2 <tool id="nanocompore_sampcomp" name="SampComp" version="@TOOL_VERSION@+galaxy1">
3 <description>to compare Nanopolished datasets</description> 3 <description>to compare Nanopolished datasets</description>
4 <expand macro="bio_tools"/> 4 <expand macro="bio_tools"/>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
19 #for $i, $current in enumerate($file2_rep) 19 #for $i, $current in enumerate($file2_rep)
20 ln -s '$current.file' 'sample_2_${i}.tsv' && 20 ln -s '$current.file' 'sample_2_${i}.tsv' &&
21 ln -s '$current.index' 'sample_2_${i}.tsv.idx' && 21 ln -s '$current.index' 'sample_2_${i}.tsv.idx' &&
22 #end for 22 #end for
23 23
24 ## symlink fasta file because a .fai file is created
25 ln -s '$fasta' reference.fa &&
26
24 ## run 27 ## run
25 nanocompore sampcomp 28 nanocompore sampcomp
26 ## required 29 ## required
27 --label1 '$label1' 30 --label1 '$label1'
28 #set files1 = ','.join(['sample_1_' + str(item) + '.tsv' for item in range(len($file1_rep))]) 31 #set files1 = ','.join(['sample_1_' + str(item) + '.tsv' for item in range(len($file1_rep))])
29 --file_list1 '$files1' 32 --file_list1 '$files1'
30 --label2 '$label2' 33 --label2 '$label2'
31 #set files2 = ','.join(['sample_2_' + str(item) + '.tsv' for item in range(len($file2_rep))]) 34 #set files2 = ','.join(['sample_2_' + str(item) + '.tsv' for item in range(len($file2_rep))])
32 --file_list2 '$files2' 35 --file_list2 '$files2'
33 --fasta '$fasta' 36 --fasta reference.fa
34 ## optional 37 ## optional
35 #if $ap.bed 38 #if $ap.bed
36 --bed '$ap.bed' 39 --bed '$ap.bed'
37 #end if 40 #end if
38 --max_invalid_kmers_freq $ap.max_invalid_kmers_freq 41 --max_invalid_kmers_freq $ap.max_invalid_kmers_freq