Mercurial > repos > matthias > daa2rma

annotate daa2rma.xml @ 2:102d29c7c5a7 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/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit 20ad8976adec9d011d21484859258bf1ad22f42e-dirty
author matthias
date Wed, 19 Dec 2018 04:44:10 -0500
parents 2ac9f9b9dd63
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
102d29c7c5a7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit 20ad8976adec9d011d21484859258bf1ad22f42e-dirty
matthias
parents: 0
diff changeset
1 <tool id="daa2rma" name="daa2rma" version="@TOOL_VERSION@" profile="19.01">
0
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
2 <description>Compute a MEGAN rma6 file from a DIAMOND daa file</description>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
3 <macros>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
4 <import>macros.xml</import>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
5 </macros>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
6 <expand macro="requirements"/>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
7 <expand macro="stdio"/>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
8 <expand macro="version_command"/>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
9 <command detect_errors="aggressive"><![CDATA[
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
10 @CLASSIFICATION_UTILS@
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
11
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
12 #set CATEGORIES=['gi2', 'acc2', 'syn2', 'tags4']
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
13 #set TARGETS=['taxa', 'eggnog', 'interpro2go', 'seed', 'kegg']
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
14
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
15 ln -s $in input.daa &&
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
16 daa2rma
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
17 -i input.daa
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
18 -o '$rma'
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
19
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
20 @MDF_CLI@
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
21 @READS_CLI@
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
22 --pairedReadsInOneFile $reads.pairedReadsInOneFile
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
23 @PARAMETERS_CLI@
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
24 --maxMatchesPerRead $params.maxMatchesPerRead
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
25 @CLASSIFICATION_CLI@
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
26 @OTHER_CLI@
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
27 ]]></command>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
28 <inputs>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
29 <param argument="--in" type="data" format="daa" label="Input DAA file"/>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
30 <expand macro="mdf_macro"/>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
31 <expand macro="reads_macro">
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
32 <param argument="--pairedReadsInOneFile" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Paired reads in one file" help="usually they are in two" />
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
33 </expand>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
34 <expand macro="params_macro">
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
35 <param argument="--maxMatchesPerRead" type="integer" value="100" label="Max matches per read" />
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
36 </expand>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
37 <expand macro="classification_macro"/>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
38 <expand macro="other_macro"/>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
39 </inputs>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
40 <outputs>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
41 <data name="rma" format="rma6" label="${tool.name} on ${on_string}"/>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
42 </outputs>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
43 <tests>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
44 <test>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
45 <param name="in" ftype="daa" value="diamond_results.daa"/>
2
102d29c7c5a7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit 20ad8976adec9d011d21484859258bf1ad22f42e-dirty
matthias
parents: 0
diff changeset
46 <output name="rma" ftype="rma6" value="diamond_results.rma" compare="sim_size" />
0
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
47 </test>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
48 </tests>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
49 <help><![CDATA[
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
50 Compute a MEGAN RMA6 file from a DIAMOND DAA file
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
51
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
52 **Input**
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
53
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
54 - DAA file
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
55 - metadata mapping file (as defined in http://qiime.org/documentation/file_formats.html
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
56 - BIOM 1 format (see http://biom-format.org/documentation/format-versions/biom-1.0.html
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
57
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
58 **Output**
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
59
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
60 - RMA6 file
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
61
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
62 ]]></help>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
63 <expand macro="citations"/>
2ac9f9b9dd63 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff changeset
64 </tool>