Mercurial > repos > ximgchess > chap_test_20230411

annotate chap/chap.xml @ 141:df35a4e87a28 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 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
author ximgchess
date Mon, 26 Jun 2023 11:55:59 +0000
parents 47b86f77fa59
children 1a292fcf3909
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
140
47b86f77fa59 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 133
diff changeset
1 <tool id="CHAP_test" name="CHESS Analysis Pipeline" version="@TOOL_VERSION@+galaxy1" 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" />
140
47b86f77fa59 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 133
diff changeset
7 <requirement type="package" version="1.0.1">nexusformat</requirement>
47b86f77fa59 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 133
diff changeset
8 <requirement type="package" version="2023.3.0">pyfai</requirement>
47b86f77fa59 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 133
diff changeset
9 <requirement type="package" version="1.10.7">pydantic</requirement>
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
10 </requirements>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
140
47b86f77fa59 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 133
diff changeset
12 pip --exists-action i install certif-pyspec==1.5.3 &&
47b86f77fa59 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 133
diff changeset
13 cd $indir &&
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
14 CHAP --config '$config' &&
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
15 ]]></command>
140
47b86f77fa59 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 133
diff changeset
16 <environment_variables>
47b86f77fa59 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 133
diff changeset
17 <environment_variable name="PYTHONPATH">/home/chess_chapaas/chess/chap/</environment_variable>
47b86f77fa59 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 133
diff changeset
18 </environment_variables>
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
19 <inputs>
140
47b86f77fa59 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 133
diff changeset
20 <param type="data" name="config" format="yaml" label="Pipeline Configuration File" />
47b86f77fa59 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 133
diff changeset
21 <param type="text" name="indir" label="Input Directory" />
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
22 </inputs>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
23 <outputs>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
24 <data name="output" format="json" />
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
25 </outputs>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
26 <tests>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
27 <test>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
28 <param name="config" value="config.yaml"/>
140
47b86f77fa59 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty
ximgchess
parents: 133
diff changeset
29 <param name="indir" value="/tmp/"/>
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
30 </test>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
31 </tests>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
32 <help><![CDATA[
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
33 CHESS Analysis Pipeline (CHAP):
0
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
ximgchess
parents:
diff changeset
34
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
35 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
36 CHAP --config CONFIG
0
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
ximgchess
parents:
diff changeset
37
133
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
38 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
39 required configuration pipeline and necessary data.
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
40 ]]></help>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
41 <citations>
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
42 <expand macro="chap-citation" />
49985da419b8 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
ximgchess
parents: 128
diff changeset
43 </citations>
0
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
ximgchess
parents:
diff changeset
44 </tool>