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annotate snap.xml @ 0:9498d2b6ae92 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
author iuc
date Fri, 10 May 2019 08:50:55 -0400
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children bcd4a1511550
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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1 <tool id="snap" name="SNAP" profile="16.04" version="@VERSION@">
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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2 <description>gene prediction</description>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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3 <macros>
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4 <import>macros.xml</import>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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5 </macros>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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6 <expand macro="requirements"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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7 <command detect_errors="aggressive"><![CDATA[
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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8 snap
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9 -gff
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10 $lcmask
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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11 #if $strand == 'forward'
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12 -plus
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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13 #else if $strand == 'backward'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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14 -minus
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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15 #end if
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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16 -aa '${output_aa}'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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17 -tx '${output_tx}'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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18 '${model}'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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19 '${input_genome}'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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20 > '${output_gff}'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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21 ]]>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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22 </command>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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23 <inputs>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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24 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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25
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26 <param name="model" type="data" format="snaphmm" label="Prediction model" help="File created with 'Train SNAP' tool"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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27
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28 <param argument="-lcmask" type="boolean"
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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29 label="Treat lowercase as N"
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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30 truevalue="-lcmask" falsevalue="" checked="false" />
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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31
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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32 <param name="strand" type="select"
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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33 label="Predict genes on specific strands">
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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34 <option value="both">both</option>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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35 <option value="forward">forward</option>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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36 <option value="backward">backward</option>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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37 </param>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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38 </inputs>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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39 <outputs>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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40 <data format="gff" name="output_gff" label="${tool.name} on ${on_string}: GFF"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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41 <data format="fasta" name="output_aa" label="${tool.name} on ${on_string}: Protein sequence"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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42 <data format="fasta" name="output_tx" label="${tool.name} on ${on_string}: Coding sequence"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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43 </outputs>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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44 <tests>
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45 <test>
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46 <param name="input_genome" value="human.fa" ftype="fasta" />
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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47 <param name="model" value="snap.hmm" />
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48 <!-- FIXME ftype temporarily removed because the not yet existing snaphmm type breaks travis tests -->
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49 <!--param name="model" value="snap.hmm" ftype="snaphmm" /-->
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50 <output name="output_gff" file="snap_annot.gff" ftype="gff"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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51 <output name="output_aa" file="annot_aa.fasta" ftype="fasta"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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52 <output name="output_tx" file="annot_tx.fasta" ftype="fasta"/>
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53 </test>
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54 </tests>
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55 <help>
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56 <![CDATA[
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57 SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.
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58 ]]>
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59 </help>
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60 <expand macro="citations"/>
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61 </tool>