Mercurial > repos > brinkmanlab > colombo

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