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comparison isescan.xml @ 0:cecb2758ec26 draft

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planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
author pimarin
date Tue, 23 Aug 2022 10:01:31 +0000
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-1:000000000000 0:cecb2758ec26
1 <tool id="isescan" name="ISEScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description> Insertion Sequence Elements detection in prokaryotic genomes </description>
3 <macros>
4 <import>macro.xml</import>
5 </macros>
6 <expand macro='xrefs'/>
7 <expand macro="requirements" />
8 <expand macro="version_command" />
9 <command detect_errors="exit_code"><![CDATA[
10 isescan.py
11 --seqfile '$input_file'
12 --output 'results'
13 $remove_short_is
14 --nthread \${GALAXY_SLOTS:-7}
15 | tee '$logfile'
16
17 ]]>
18 </command>
19 <inputs>
20 <param name="input_file" type="data" format="fasta,fasta.gz" label="Genome fasta input" help="Fasta sequence to analyse for IS"/>
21 <param name="remove_short_is" argument="--removeShortIS" type="boolean" truevalue="--removeShortIS" falsevalue=""
22 label="Remove incomplete IS elements"
23 help="Remove partial IS elements which include IS element with length &gt; 400 or single copy IS element without perfect TIR"/>
24 <param name="output_format" type="select" label="Output format type" help="Choose an output file format">
25 <option value="raw"> Raw format (txt) </option>
26 <option value="csv"> Coma separate file (CSV) </option>
27 <option value="tsv" selected="true"> Tabular separate file (TSV) </option>
28 </param>
29 <param name="log_activate" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Keep the log file"/>
30 </inputs>
31 <outputs>
32 <data name="summary" format="txt" label="${tool.name} on ${on_string}: Summary of detected IS"/>
33 <data name="is_results" format="tabular" label="${tool.name} on ${on_string}: IS detected">
34 <change_format>
35 <when input="output_format" value="raw" format="txt"/>
36 <when input="output_format" value="csv" format="csv"/>
37 <when input="output_format" value="tsv" format="tabular"/>
38 </change_format>
39 </data>
40 <data name="gff_file" format="gff3" label="IS annotation"/>
41 <data name="is_fasta" format="fasta" label="${tool.name} on ${on_string}: IS nucleic sequence"/>
42 <data name="tpase_fasta" format="fasta" label="${tool.name} on ${on_string}: Transposase nucleic acid sequence"/>
43 <data name="tpase_amino" format="fasta" label="${tool.name} on ${on_string}: Transposase amino acid sequence"/>
44 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: Log file">
45 <filter> log_activate == True </filter>
46 </data>
47 </outputs>
48 <tests>
49 <test> <!-- TEST_1 default parameters -->
50 <param name="input_file" value="NC_012624.fna" />
51 <output name="summary" value="TEST_1/test_1.fna.sum"/>
52 <output name="is_results" value="TEST_1/test_1.fna.tsv"/>
53 <output name="gff_file" value="TEST_1/test_1.fna.gff"/>
54 <output name="is_fasta" value="TEST_1/test_1.fna.is.fna"/>
55 <output name="tpase_fasta" value="TEST_1/test_1.fna.orf.fna"/>
56 <output name="tpase_amino" value="TEST_1/test_1.fna.orf.faa"/>
57 <output name="logfile" value="TEST_1/test_1.log" lines_diff="50"/>
58 </test>
59 <test> <!-- TEST_2 with remove_short_is and raw output-->
60 <param name="input_file" value="NC_012624.fna"/>
61 <param name="remove_short_is" value="true"/>
62 <param name="output_format" value="raw"/>
63 <output name="summary" value="TEST_2/test_2.fna.sum"/>
64 <output name="is_results" value="TEST_2/test_2.fna.raw"/>
65 <output name="gff_file" value="TEST_2/test_2.fna.gff"/>
66 <output name="is_fasta" value="TEST_2/test_2.fna.is.fna"/>
67 <output name="tpase_fasta" value="TEST_2/test_2.fna.orf.fna"/>
68 <output name="tpase_amino" value="TEST_2/test_2.fna.orf.faa"/>
69 <output name="logfile" value="TEST_2/test_2.log" lines_diff="50"/>
70 </test>
71 <test> <!-- TEST_3 without logfile and with csv output-->
72 <param name="input_file" value="NC_012624.fna"/>
73 <param name="remove_short_is" value="false"/>
74 <param name="output_format" value="csv"/>
75 <param name="log_activate" value="False"/>
76 <output name="summary" value="TEST_3/test_3.fna.sum"/>
77 <output name="is_results" value="TEST_3/test_3.fna.tsv"/>
78 <output name="gff_file" value="TEST_3/test_3.fna.gff"/>
79 <output name="is_fasta" value="TEST_3/test_3.fna.is.fna"/>
80 <output name="tpase_fasta" value="TEST_3/test_3.fna.orf.fna"/>
81 <output name="tpase_amino" value="TEST_3/test_3.fna.orf.faa"/>
82 </test>
83 </tests>
84 <help><![CDATA[
85 **What it does**
86 With
87 ]]>
88 </help>
89 <expand macro="citations"/>
90 </tool>