Mercurial > repos > ximgchess > hedm_npz_to_tesr

annotate hedm_npz_to_tesr.xml @ 1:e90d5493a744 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit f763b826a9f29b649e0d24b3d7765b292f26e2fa"
author ximgchess
date Thu, 07 Jul 2022 18:47:53 +0000
parents bd74229f61e8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
e90d5493a744 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit f763b826a9f29b649e0d24b3d7765b292f26e2fa"
ximgchess
parents: 0
diff changeset
1 <tool id="hedm_npz_to_tesr" name="HEDM to tesr" version="1.0.0" python_template_version="3.5">
0
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
2 <description>Convert HEDM npz to a Neper tesr</description>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
3 <requirements>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
4 <requirement type="package" version="1.19">numpy</requirement>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
5 </requirements>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
7 $__tool_directory__/hedm_npz_to_tesr.py
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
8 --voxel_spacing $voxel_spacing
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
9 #if $names.x_name:
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
10 -x '$names.x_name'
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
11 #end if
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
12 #if $names.y_name:
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
13 -y '$names.y_name'
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
14 #end if
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
15 #if $names.z_name:
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
16 -z '$names.z_name'
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
17 #end if
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
18 #if $names.grain_map:
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
19 --grain_map '$names.grain_map'
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
20 #end if
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
21 '$input'
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
22 '$output'
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
23 ]]></command>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
24 <inputs>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
25 <!-- change format to approriate npz subclass when available -->
1
e90d5493a744 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit f763b826a9f29b649e0d24b3d7765b292f26e2fa"
ximgchess
parents: 0
diff changeset
26 <param name="input" type="data" format="npz" label="HEDM npz file"/>
0
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
27 <param name="voxel_spacing" type="float" value="0.005" min="0" label="Voxel spacing"/>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
28 <section name="names" expanded="false" title="Specify names used in HEDM.npz input file">
1
e90d5493a744 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit f763b826a9f29b649e0d24b3d7765b292f26e2fa"
ximgchess
parents: 0
diff changeset
29 <param name="x_name" type="text" value="" label="Name of the X array in the input" optional="true" help="Default is a name containing 'X'"/>
e90d5493a744 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit f763b826a9f29b649e0d24b3d7765b292f26e2fa"
ximgchess
parents: 0
diff changeset
30 <param name="y_name" type="text" value="" label="Name of the Y array in the input" optional="true" help="Default is a name containing 'Y'"/>
e90d5493a744 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit f763b826a9f29b649e0d24b3d7765b292f26e2fa"
ximgchess
parents: 0
diff changeset
31 <param name="z_name" type="text" value="" label="Name of the Z array in the input" optional="true" help="Default is a name containing 'Z'"/>
e90d5493a744 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit f763b826a9f29b649e0d24b3d7765b292f26e2fa"
ximgchess
parents: 0
diff changeset
32 <param name="grain_map" type="text" value="" label="Name of the grain map in the input" optional="true" help="Default is a name containing 'grain'"/>
0
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
33 </section>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
34 </inputs>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
35 <outputs>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
36 <!-- output format should be changed to tesr when that is available -->
1
e90d5493a744 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit f763b826a9f29b649e0d24b3d7765b292f26e2fa"
ximgchess
parents: 0
diff changeset
37 <data name="output" format="neper.tesr" label="${input.name.rsplit(sep='.',maxsplit=1)[0]}.tesr"/>
0
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
38 </outputs>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
39 <tests>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
40 <test>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
41 <!-- change format to approriate npz subclass when available -->
1
e90d5493a744 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit f763b826a9f29b649e0d24b3d7765b292f26e2fa"
ximgchess
parents: 0
diff changeset
42 <param name="input" ftype="npz" value="HEDM_map.npz"/>
0
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
43 <output name="output" file="HEDM_map.tesr"/>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
44 </test>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
45 </tests>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
46 <help><![CDATA[
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
47 Create a neper compatible tesr format file from a HEDM numpy compressed file.
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
48 The converter will look for columns named: Xs, Ys, Zs, and grain_map by default,
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
49 If the input file uses different names, the user should specify them.
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
50 ]]></help>
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
51 </tool>