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comparison SigiHMM.xml @ 0:7fe2bd997c49 draft default tip

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/colombo commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
author brinkmanlab
date Fri, 24 Jan 2020 17:33:58 -0500
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-1:000000000000 0:7fe2bd997c49
1 <tool id="sigihmm" name="SigiHMM" version="3.8.0" profile="16.04">
2 <description>Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models</description>
3 <edam_topics>
4 <edam_topic>topic_0194</edam_topic>
5 <edam_topic>topic_0091</edam_topic>
6 </edam_topics>
7 <edam_operations>
8 <edam_operation>operation_0362</edam_operation>
9 </edam_operations>
10 <requirements>
11 <requirement type="package" version="3.8">colombo</requirement>
12 </requirements>
13 <version_command><![CDATA[ echo "3.8" ]]></version_command>
14 <command detect_errors="exit_code"><![CDATA[
15 #import os
16 #set input_l=$os.path.basename(str($input))+".embl"
17 #set output_l=$os.path.basename(str($output))+".embl"
18 ln -sf "$input" "$input_l" &&
19 ln -sf "$output" "$output_l" &&
20 #if $cut
21 #set cut_l=$os.path.basename(str($cut))+".cut"
22 ln -sf "$cut" "$cut_l" &&
23 #end if
24 #set gff_l=$os.path.basename(str($gff))+".gff"
25 ln -sf "$gff" "$gff_l" &&
26
27 SigiHMM input="`pwd`/$input_l" output="`pwd`/$output_l" sens=$sens outlier=$outlier phx=$phx join=$join gff="`pwd`/$gff_l"
28 #if $cut
29 cut="`pwd`/$cut_l"
30 #end if
31 ]]></command>
32 <inputs>
33 <param type="data" format="embl" name="input" argument="input" label="Input" optional="false" />
34 <param type="data" format="cut" name="cut" argument="cut" label="Donor candidates CUT file" optional="true" />
35 <param type="float" name="sens" argument="sens" label="PUTAL Sensitivity" optional="false" min="0" max="1.0" value="0.7" />
36 <param type="boolean" name="outlier" argument="outlier" label="Assess Outliers" optional="false" truevalue="Yes" falsevalue="No" checked="false" />
37 <param type="boolean" name="phx" argument="phx" label="Assess PHX" optional="false" truevalue="Yes" falsevalue="No" checked="true" />
38 <param type="select" name="join" argument="join" label="Merge Islands Of Distance" optional="false" >
39 <option value="0">0</option>
40 <option value="1" selected="true">1</option>
41 <option value="2">2</option>
42 <option value="3">3</option>
43 </param>
44 </inputs>
45 <outputs>
46 <data format="embl" name="output" metadata_source="input" />
47 <data format="gff" name="gff" label="${tool.name} on ${on_string} features" />
48 </outputs>
49 <tests>
50 <test expect_num_outputs="2">
51 <!-- SigiHMM uses biojava which currently has a bug: https://github.com/biojava/biojava/issues/843 -->
52 <param name="input" value="test-data/test.embl" ftype="embl" />
53 <param name="join" value="3" />
54 <output name="output" checksum="sha256:f87830fad329a0c47f734cffa069593be0423a064878bd894df8b8dc4b451c3d" ftype="embl" />
55 <output name="gff" checksum="sha256:6af8fb320804803f54870c3e7b024d5e1305cee7e464e89355fba1f00f94ce44" ftype="gff" />
56 </test>
57 <test expect_failure="true">
58 <!-- SigiHMM 3.8 crashes for an unknown reason on some datasets. v4.0 does not seem to have this issue. -->
59 <param name="input" value="test-data/crash.embl" ftype="embl" />
60 <param name="join" value="3" />
61 </test>
62 </tests>
63 <help><![CDATA[
64 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-142
65 ]]></help>
66 <citations>
67 <citation type="doi">10.5281/zenodo.3364789</citation>
68 <citation type="doi">10.1186/1471-2105-7-142</citation>
69 </citations>
70 </tool>