Mercurial > repos > iuc > nanocompore_sampcomp
comparison sampcomp.xml @ 4:c0fb573c1e8d draft default tip
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 |
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| 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 |