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comparison MIRUReader.xml @ 1:1a7d6584e1ec draft

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author dcouvin
date Tue, 17 Aug 2021 23:27:22 +0000
parents f0e3646a4e45
children f9422a33e9c1
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0:f0e3646a4e45 1:1a7d6584e1ec
1 <tool id="mirutool" name="mirureader" version="6.6.0"> 1 <tool id="mirureader" name="mirureader" version="1.0.0">
2 <description> MIRUReader.... </description> 2 <description> MIRUReader allows to perform in-silico MIRU-VNTR typing using long reads or assembled genome </description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.2.0">python3-openid</requirement> 5 <requirement type="package" version="3.2.0">python3-openid</requirement>
6 <requirement type="package" version="6.6.0">emboss</requirement> 6 <requirement type="package" version="6.6.0">emboss</requirement>
7 <requirement type="package" version="1.3.2">pandas</requirement> 7 <requirement type="package" version="1.3.2">pandas</requirement>
8 </requirements> 8 </requirements>
9 9
10 <command>cp $input input.fasta; python3 $__tool_directory__/MIRUReader/MIRUReader.py -r input.fasta -p name 1> $output 2>$logfile</command> 10 <!--<command>cp $input input.fasta; python3 $__tool_directory__/MIRUReader/MIRUReader.py -r input.fasta -p sample 1> $output 2>$logfile</command>-->
11 <!-- 11
12 <command interpreter="bash" detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 13
14 #import re 14 #import re
15 ## Creates symlinks for each input file based on the Galaxy 'element_identifier' 15 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
16 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') 16 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
17 #set $named_input_files = '' 17
18 #for $input_file in $input_files 18 ## Add single quotes around each input file identifier
19 ## Add single quotes around each input file identifier 19 #set $_input_file = "'{}'".format($input.element_identifier)
20 #set $_input_file = "'{}'".format($input_file.element_identifier) 20 #set $_input_file = $_input_file + '.fasta'
21 ln -s '${input_file}' ${_input_file} && 21 ln -s '${input}' ${_input_file} &&
22 #set $named_input_files = $named_input_files + ' ' + $_input_file
23 #end for
24 22
25 #for $element in $named_input_files 23 python3 $__tool_directory__/MIRUReader/MIRUReader.py -r $_input_file -p $_input_file > $output
26 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $element '-p' $element > $output 24
27 #end for
28 25
29 26
30 27
31 ]]></command> 28 ]]></command>
32 -->
33 29
34 <!-- for element in `echo $named_input_files`; do python3 MIRUReader.py -r $element -p $element;done > $output 30 <!-- for element in `echo $named_input_files`; do python3 MIRUReader.py -r $element -p $element;done > $output
35 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $named_input_files '-p' $named_input_files > $output --> 31 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $named_input_files '-p' $named_input_files > $output -->
36 32
37 <inputs> 33 <inputs>
38 <!-- 34 <!--
39 <param format="fasta" name="input_files" type="data" label="fasta files :" multiple="true" display="checkboxes"/> 35 <param format="fasta" name="input_files" type="data" label="fasta files :" multiple="true" display="checkboxes"/>
40 --> 36 -->
41 <param format="fasta" name="input" type="data" label="Fasta file"/> 37 <param format="fasta" name="input" type="data" label="Fasta file"/>
42 </inputs> 38 </inputs>
43 39
44 <outputs> 40 <outputs>
45 <data format="tabular" name="output" label="MIRUreader output"/> 41 <data format="tabular" name="output" label="MIRUReader output"/>
46 <data format="txt" name="logfile" label="Logfile"/> 42 <!--<data format="txt" name="logfile" label="LogFile"/>-->
47 </outputs> 43 </outputs>
48 44
49 <help> 45 <help><![CDATA[
50 -Git:https://github.com/phglab/MIRUReader.git 46 MIRUReader allows to identify 24-locus MIRU-VNTR for Mycobacterium tuberculosis complex (MTBC) directly from long reads generated by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio). It also work on assembled genome.
51 </help> 47
48 GitHub: https://github.com/phglab/MIRUReader.git
49 ]]>
50 </help>
52 51
53 <citations> 52 <citations>
54 <citation type="doi">10.1093/bioinformatics/btz771</citation> 53 <citation type="doi">10.1093/bioinformatics/btz771</citation>
55 </citations> 54 </citations>
56 </tool> 55 </tool>