annotate macros.xml @ 1:8c30496a665a draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
author galaxyp
date Wed, 23 Sep 2020 17:01:47 +0000
parents 6cfd42b015b4
children 944b43462104
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
1 <macros>
1
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
2 <token name="@VERSION@">2.0.0</token>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
3 <token name="@GVERSION@">2.0.0-0</token>
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
4 <xml name="requirements">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
5 <requirements>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
6 <requirement type="package" version="@VERSION@">metaquantome</requirement>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
7 <yield/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
8 </requirements>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
9 </xml>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
10 <xml name="db">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
11 <param argument="db_tar" type="data" label="Database Archive File"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
12 </xml>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
13 <xml name="ONTOLOGY_ARGS">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
14 <conditional name="ontology_args">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
15 <param name="ontology" type="select" label="Ontology">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
16 <option value="go">Gene Ontology (GO terms)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
17 <option value="ec">Enzyme Commission (EC) numbers</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
18 <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
19 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
20 <when value="go">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
21 <param argument="--slim_down" type="boolean" label="Use slim GO"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
22 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
23 <when value="ec">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
24 <!-- do nothing -->
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
25 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
26 <when value="cog">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
27 <!-- do nothing -->
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
28 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
29 </conditional>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
30 </xml>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
31 <token name="@COMMON_PARAMS@"><![CDATA[
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
32 --samps '$samps'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
33 --mode '$mode_args.mode'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
34 #if $mode_args.mode == 'f'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
35 --ontology='$mode_args.ontology_args.ontology'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
36 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
37 #if $mode_args.mode == 'ft'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
38 --ontology='$mode_args.ontology_args.ontology'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
39 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
40 ]]>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
41 </token>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
42 <xml name="SAMPS">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
43 <param name="samps" type="data" format="tabular" label="Samples file"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
44 help="must be created by 'metaQuantome: create samples file'"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
45 </xml>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
46 <xml name="citations">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
47 <citations>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
48 <yield />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
49 </citations>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
50 </xml>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
51 </macros>