annotate macros.xml @ 6:35cc7ca0bdc7 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
author galaxyp
date Mon, 18 Mar 2024 12:35:03 +0000
parents a1daafbf5233
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
1 <macros>
5
a1daafbf5233 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 12499da76192d2a61bfd475bc6e21dbe6f23643a"
galaxyp
parents: 4
diff changeset
2 <token name="@TOOL_VERSION@">2.0.2</token>
4
deaf035bbe9f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 9204193c3442e427c149b90f15fe3a56fc9802e9"
galaxyp
parents: 3
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
6
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
4 <xml name="xrefs">
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
5 <xrefs>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
6 <xref type="bio.tools">metaQuantome</xref>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
7 </xrefs>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
8 </xml>
0
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
9 <xml name="requirements">
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
10 <requirements>
6
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
11 <requirement type="package" version="@TOOL_VERSION@">metaquantome</requirement>
0
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
12 <yield/>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
13 </requirements>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
14 </xml>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
15 <xml name="db">
6
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
16 <param argument="db_tar" type="data" label="Database Archive File"/>
0
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
17 </xml>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
18 <xml name="ONTOLOGY_ARGS">
6
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
19 <conditional name="ontology_args">
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
20 <param name="ontology" type="select" label="Ontology">
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
21 <option value="go">Gene Ontology (GO terms)</option>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
22 <option value="ec">Enzyme Commission (EC) numbers</option>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
23 <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
24 </param>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
25 <when value="go">
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
26 <param argument="--slim_down" type="boolean" label="Use slim GO"/>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
27 </when>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
28 <when value="ec">
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
29 <!-- do nothing -->
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
30 </when>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
31 <when value="cog">
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
32 <!-- do nothing -->
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
33 </when>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
34 </conditional>
0
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
35 </xml>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
36 <token name="@COMMON_PARAMS@"><![CDATA[
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
37 --samps '$samps'
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
38 --mode '$mode_args.mode'
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
39 #if $mode_args.mode == 'f'
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
40 --ontology='$mode_args.ontology_args.ontology'
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
41 #end if
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
42 #if $mode_args.mode == 'ft'
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
43 --ontology='$mode_args.ontology_args.ontology'
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
44 #end if
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
45 ]]>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
46 </token>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
47 <xml name="SAMPS">
6
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
48 <param name="samps" type="data" format="tabular" label="Samples file" help="must be created by 'metaQuantome: create samples file'"/>
0
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
49 </xml>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
50 <xml name="citations">
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
51 <citations>
6
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
52 <citation type="doi">10.1021/ACS.JPROTEOME.0C00960</citation>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
galaxyp
parents: 5
diff changeset
53 <yield/>
0
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
54 </citations>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
55 </xml>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
56 </macros>