Mercurial > repos > iuc > nanocompore_sampcomp

comparison sampcomp.xml @ 4:c0fb573c1e8d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 51078f4c0eab9cc41a0cb2190000e428322631a4
author iuc
date Thu, 23 Jun 2022 17:29:34 +0000
parents 25abc2c72ff9
children
comparison
equal deleted inserted replaced
3:b833eff63b10 4:c0fb573c1e8d
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 <macros> 5 <macros>
5 <import>macros.xml</import> 6 <import>macros.xml</import>
6 </macros> 7 </macros>
7 <expand macro="requirements"/> 8 <expand macro="requirements"/>
8 <version_command><![CDATA[nanocompore --version]]></version_command> 9 <version_command><![CDATA[nanocompore --version]]></version_command>
18 #for $i, $current in enumerate($file2_rep) 19 #for $i, $current in enumerate($file2_rep)
19 ln -s '$current.file' 'sample_2_${i}.tsv' && 20 ln -s '$current.file' 'sample_2_${i}.tsv' &&
20 ln -s '$current.index' 'sample_2_${i}.tsv.idx' && 21 ln -s '$current.index' 'sample_2_${i}.tsv.idx' &&
21 #end for 22 #end for
22 23
24 ## symlink fasta file because a .fai file is created
25 ln -s '$fasta' reference.fa &&
26
23 ## run 27 ## run
24 nanocompore sampcomp 28 nanocompore sampcomp
25 ## required 29 ## required
26 --label1 '$label1' 30 --label1 '$label1'
27 #set files1 = ','.join(['sample_1_' + str(item) + '.tsv' for item in range(len($file1_rep))]) 31 #set files1 = ','.join(['sample_1_' + str(item) + '.tsv' for item in range(len($file1_rep))])
28 --file_list1 '$files1' 32 --file_list1 '$files1'
29 --label2 '$label2' 33 --label2 '$label2'
30 #set files2 = ','.join(['sample_2_' + str(item) + '.tsv' for item in range(len($file2_rep))]) 34 #set files2 = ','.join(['sample_2_' + str(item) + '.tsv' for item in range(len($file2_rep))])
31 --file_list2 '$files2' 35 --file_list2 '$files2'
32 --fasta '$fasta' 36 --fasta reference.fa
33 ## optional 37 ## optional
34 #if $ap.bed 38 #if $ap.bed
35 --bed '$ap.bed' 39 --bed '$ap.bed'
36 #end if 40 #end if
37 --max_invalid_kmers_freq $ap.max_invalid_kmers_freq 41 --max_invalid_kmers_freq $ap.max_invalid_kmers_freq