Mercurial > repos > iuc > snap

annotate snap.xml @ 1:bcd4a1511550 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:38:29 +0000
parents 9498d2b6ae92
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
2 <description>gene prediction</description>
1
bcd4a1511550 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 0
diff changeset
3 <xrefs>
bcd4a1511550 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 0
diff changeset
4 <xref type="bio.tools">snap</xref>
bcd4a1511550 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 0
diff changeset
5 </xrefs>
0
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
6 <macros>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
7 <import>macros.xml</import>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
8 </macros>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
9 <expand macro="requirements"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
10 <command detect_errors="aggressive"><![CDATA[
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
11 snap
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
12 -gff
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
13 $lcmask
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
14 #if $strand == 'forward'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
15 -plus
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
16 #else if $strand == 'backward'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
17 -minus
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
18 #end if
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
19 -aa '${output_aa}'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
20 -tx '${output_tx}'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
21 '${model}'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
22 '${input_genome}'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
23 > '${output_gff}'
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
24 ]]>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
25 </command>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
26 <inputs>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
27 <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
iuc
parents:
diff changeset
28
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
29 <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
iuc
parents:
diff changeset
30
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
31 <param argument="-lcmask" type="boolean"
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
32 label="Treat lowercase as N"
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
33 truevalue="-lcmask" falsevalue="" checked="false" />
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
34
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
35 <param name="strand" type="select"
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
36 label="Predict genes on specific strands">
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
37 <option value="both">both</option>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
38 <option value="forward">forward</option>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
39 <option value="backward">backward</option>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
40 </param>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
41 </inputs>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
42 <outputs>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
43 <data format="gff" name="output_gff" label="${tool.name} on ${on_string}: GFF"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
44 <data format="fasta" name="output_aa" label="${tool.name} on ${on_string}: Protein sequence"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
45 <data format="fasta" name="output_tx" label="${tool.name} on ${on_string}: Coding sequence"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
46 </outputs>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
47 <tests>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
48 <test>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
49 <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
iuc
parents:
diff changeset
50 <param name="model" value="snap.hmm" />
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
51 <!-- FIXME ftype temporarily removed because the not yet existing snaphmm type breaks travis tests -->
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
52 <!--param name="model" value="snap.hmm" ftype="snaphmm" /-->
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
53 <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
iuc
parents:
diff changeset
54 <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
iuc
parents:
diff changeset
55 <output name="output_tx" file="annot_tx.fasta" ftype="fasta"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
56 </test>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
57 </tests>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
58 <help>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
59 <![CDATA[
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
60 SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
61 ]]>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
62 </help>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
63 <expand macro="citations"/>
9498d2b6ae92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
parents:
diff changeset
64 </tool>