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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:35:00 -0400
parents 9a9768ad0f81
children
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9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
chemteam
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1 # Template for packmol in Galaxy
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
chemteam
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2 #
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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4 tolerance {{ allparams.tolerance }}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
chemteam
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5 nloop {{ allparams.nloop }}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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6 maxit {{ allparams.maxit }}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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7 seed {{ allparams.seed }}
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9d1e7348f7a8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
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8 filetype pdb
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9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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9 output {{outfile}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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10
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9d1e7348f7a8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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11 {% for struct in packmol_inputs %}
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9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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12 structure {{struct.file}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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13 # Galaxy datasetname - {{struct.datasetname}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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14 number {{struct.structureparams.number}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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15 radius {{struct.structureparams.radius}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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16 resnumbers {{struct.structureparams.resnumbers}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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17 {% for c in struct.structureparams.constraints_repeat %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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18 {% if c.constraints.constraint == 'fixed' %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
chemteam
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19 {% if c.constraints.center == 'Yes' %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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20 center
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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21 {% endif %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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22 {{c.constraints.constraint}} {{c.constraints.x}} {{c.constraints.y}} {{c.constraints.z}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.g}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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23 {% elif c.constraints.constraint == 'cube' %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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24 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.xmin}} {{c.constraints.ymin}} {{c.constraints.zmin}} {{c.constraints.d}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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25 {% elif c.constraints.constraint == 'box' %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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26 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.xmin}} {{c.constraints.ymin}} {{c.constraints.zmin}} {{c.constraints.xmax}} {{c.constraints.ymax}} {{c.constraints.zmax}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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27 {% elif c.constraints.constraint == 'sphere' %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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28 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.c}} {{c.constraints.d}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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29 {% elif c.constraints.constraint == 'ellipsoid' %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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30 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a1}} {{c.constraints.b1}} {{c.constraints.c1}} {{c.constraints.a2}} {{c.constraints.b2}} {{c.constraints.c2}} {{c.constraints.d}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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31 {% elif c.constraints.constraint == 'plane' %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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32 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.c}} {{c.constraints.d}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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33 {% elif c.constraints.constraint == 'cylinder' %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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34 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a1}} {{c.constraints.b1}} {{c.constraints.c1}} {{c.constraints.a2}} {{c.constraints.b2}} {{c.constraints.c2}} {{c.constraints.d}} {{c.constraints.l}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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35 {% else %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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36 unknowntype specified {{c.constraints}}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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37 {% endif %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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38 {% endfor %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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39 end structure
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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41 {% endfor %}
9a9768ad0f81 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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