Mercurial > repos > iuc > bbtools_bbmap

annotate macros.xml @ 0:07a6e49c7d74 draft

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/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
author iuc
date Mon, 04 Oct 2021 12:14:47 +0000
parents
children e0ca2ec4f5d9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
1 <macros>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
2 <token name="@WRAPPER_VERSION@">1.0.0</token>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
3 <token name="@VERSION_SUFFIX@">1.0.0</token>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
4 <token name="@PROFILE@">20.09</token>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
5 <xml name="requirements">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
6 <requirements>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
7 <requirement type="package" version="38.92">bbmap</requirement>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
8 </requirements>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
9 </xml>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
10 <macro name="dbKeyActionsBBMap">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
11 <expand macro="dbKeyActions">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
12 <option type="from_data_table" name="fasta_indexes" column="1" offset="0">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
13 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
14 <filter type="param_value" ref="ref_source_cond.reference" column="1"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
15 </option>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
16 </expand>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
17 </macro>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
18 <macro name="dbKeyActions">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
19 <actions>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
20 <conditional name="ref_source_cond.ref_source">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
21 <when value="cached">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
22 <action type="metadata" name="dbkey">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
23 <yield/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
24 </action>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
25 </when>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
26 <when value="history">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
27 <action type="metadata" name="dbkey">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
28 <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
29 </action>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
30 </when>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
31 </conditional>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
32 </actions>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
33 </macro>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
34 <macro name="reference_source_cond">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
35 <conditional name="ref_source_cond">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
36 <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
37 <option value="cached" selected="True">Use a cached reference</option>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
38 <option value="history">Use a reference from the history</option>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
39 </param>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
40 <when value="cached">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
41 <param name="reference" type="select" label="Using reference genome">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
42 <options from_data_table="fasta_indexes">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
43 <filter type="sort_by" column="2"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
44 <validator type="no_options" message="A built-in reference genome is not available"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
45 </options>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
46 </param>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
47 </when>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
48 <when value="history">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
49 <param name="reference" type="data" format="fasta" label="Using reference genome">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
50 <validator type="no_options" message="The current history does not include a fasta dataset"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
51 </param>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
52 </when>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
53 </conditional>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
54 </macro>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
55 <xml name="citations">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
56 <citations>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
57 <citation type="doi">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
58 https://doi.org/10.1371/journal.pone.0185056
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
59 </citation>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
60 </citations>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
61 </xml>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
62 </macros>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
63