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annotate hedm_npz_to_tesr.xml @ 4:b49a8ef3351d draft

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
author ximgchess
date Thu, 01 Apr 2021 18:29:39 +0000
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b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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1 <tool id="hedm_npz_to_tesr" name="HEDM to tesr" version="0.1.0" python_template_version="3.5">
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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2 <description>Convert HEDM npz to a Neper tesr</description>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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3 <requirements>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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4 <requirement type="package" version="1.19">numpy</requirement>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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5 </requirements>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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6 <command detect_errors="exit_code"><![CDATA[
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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7 $__tool_directory__/hedm_npz_to_tesr.py
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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8 --voxel_spacing $voxel_spacing
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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9 #if $names.x_name:
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10 -x '$names.x_name'
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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11 #end if
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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12 #if $names.y_name:
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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13 -y '$names.y_name'
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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14 #end if
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15 #if $names.z_name:
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16 -z '$names.z_name'
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17 #end if
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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18 #if $names.grain_map:
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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19 --grain_map '$names.grain_map'
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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20 #end if
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21 '$input'
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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22 '$output'
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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23 ]]></command>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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24 <inputs>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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25 <!-- change format to approriate npz subclass when available -->
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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26 <param name="input" type="data" format="zip" label="HEDM npz file"/>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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27 <param name="voxel_spacing" type="float" value="0.005" min="0" label="Voxel spacing"/>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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28 <section name="names" expanded="false" title="Specify names used in HEDM.npz input file">
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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29 <param name="x_name" type="text" value="" label="Name of the X array in the input" optional="true" help="Deafault is a name containing 'X'"/>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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30 <param name="y_name" type="text" value="" label="Name of the Y array in the input" optional="true" help="Deafault is a name containing 'Y'"/>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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31 <param name="z_name" type="text" value="" label="Name of the Z array in the input" optional="true" help="Deafault is a name containing 'Z'"/>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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32 <param name="grain_map" type="text" value="" label="Name of the grain map in the input" optional="true" help="Deafault is a name containing 'grain'"/>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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33 </section>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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34 </inputs>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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35 <outputs>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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36 <!-- output format should be changed to tesr when that is available -->
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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37 <data name="output" format="txt" label="${input.name.rsplit(sep='.',maxsplit=1)[0]}.tesr"/>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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38 </outputs>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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39 <tests>
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40 <test>
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41 <!-- change format to approriate npz subclass when available -->
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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42 <param name="input" ftype="zip" value="HEDM_map.npz"/>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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43 <output name="output" file="HEDM_map.tesr"/>
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44 </test>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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45 </tests>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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46 <help><![CDATA[
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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47 Create a neper compatible tesr format file from a HEDM numpy compressed file.
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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48 The converter will look for columns named: Xs, Ys, Zs, and grain_map by default,
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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49 If the input file uses different names, the user should specify them.
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50 ]]></help>
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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51 </tool>