Mercurial > repos > mvdbeek > bam_readtagger

annotate macros.xml @ 62:16eba798cbc6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 20d187a08a5c511cb38e7e60aeadfc2962dc03d3"
author mvdbeek
date Sat, 31 Aug 2019 09:48:36 -0400
parents 301316cb596a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
1 <macros>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
2 <xml name="tag_options">
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
3 <option value="A">A</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
4 <option value="B">B</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
5 <option value="C">C</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
6 <option value="D">D</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
7 <option value="E">E</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
8 <option value="F">F</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
9 <option value="G">G</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
10 <option value="H">H</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
11 <option value="I">I</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
12 <option value="J">J</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
13 <option value="K">K</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
14 <option value="L">L</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
15 <option value="M">M</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
16 <option value="N">N</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
17 <option value="O">O</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
18 <option value="P">P</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
19 <option value="Q">Q</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
20 <option value="R">R</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
21 <option value="S">S</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
22 <option value="T">T</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
23 <option value="U">U</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
24 <option value="V">V</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
25 <option value="W">W</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
26 <option value="X">X</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
27 <option value="Y">Y</option>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
28 </xml>
31
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
29 <xml name="reference_source_conditional" token_reference_type="reference_type">
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
30 <conditional name="@REFERENCE_TYPE@_source">
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
31 <param name="reference_source_selector" type="select" label="Will you select a @REFERENCE_TYPE@ reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
32 <option value="cached">Use a built-in @REFERENCE_TYPE@ genome index</option>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
33 <option value="history">Use a genome from history and build index</option>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
34 </param>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
35 <when value="cached">
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
36 <param name="ref_file" type="select" label="Using @REFERENCE_TYPE@ reference genome" help="Select @REFERENCE_TYPE@ genome from the list" optional="True">
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
37 <options from_data_table="bwa_mem_indexes">
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
38 <filter type="sort_by" column="2" />
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
39 <validator type="no_options" message="No indexes are available" />
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
40 </options>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
41 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
42 </param>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
43 </when>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
44 <when value="history">
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
45 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" optional="True"/>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
46 </when>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
47 </conditional>
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents: 0
diff changeset
48 </xml>
0
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
parents:
diff changeset
49 </macros>