Mercurial > repos > ximgchess > chap_test_20230411

annotate chap/chap.xml @ 149:3b4cd4e35b3a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 743573b7be16eb3a159ec0affb43ea370cc190f6-dirty
author ximgchess
date Tue, 27 Jun 2023 12:12:03 +0000
parents 807ef54fdc76
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
144
807ef54fdc76 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 143
diff changeset
1 <tool id="CHAP_test" name="CHESS Analysis Pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
2 <macros>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
3 <import>../macros.xml</import>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
4 </macros>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
5 <requirements>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
6 <expand macro="chap-requirement" />
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
7 </requirements>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
144
807ef54fdc76 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 143
diff changeset
9 cp '$input' data.csv &&
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
10 CHAP --config '$config' &&
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
11 ]]></command>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
12 <inputs>
144
807ef54fdc76 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 143
diff changeset
13 <param type="data" name="config" format="yaml" />
807ef54fdc76 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 143
diff changeset
14 <param type="data" name="input" format="csv" />
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
15 </inputs>
144
807ef54fdc76 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 143
diff changeset
16 <outputs>
807ef54fdc76 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 143
diff changeset
17 <data name="output" format="json" />
807ef54fdc76 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 143
diff changeset
18 </outputs>
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
19 <tests>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
20 <test>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
21 <param name="config" value="config.yaml"/>
144
807ef54fdc76 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 143
diff changeset
22 <param name="input" value="data.csv"/>
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
23 </test>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
24 </tests>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
25 <help><![CDATA[
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
26 CHESS Analysis Pipeline (CHAP):
0
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
ximgchess
parents:
diff changeset
27
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
28 To run it on command line you'll use:
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
29 CHAP --config CONFIG
0
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
ximgchess
parents:
diff changeset
30
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
31 To run it within galaxy you'll only need to upload your
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
32 required configuration pipeline and necessary data.
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
33 ]]></help>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
34 <citations>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
35 <expand macro="chap-citation" />
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
36 </citations>
0
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
ximgchess
parents:
diff changeset
37 </tool>