Mercurial > repos > chemteam > bio3d_pca
annotate pca.xml @ 5:24867ab16f36 draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:45:05 -0400 |
| parents | 54dd1596e04e |
| children |
| rev | line source |
|---|---|
|
0
f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
|
1 <tool id="bio3d_pca" name="PCA" version="@VERSION@"> |
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5
24867ab16f36
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
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2 <description>- principal component analysis using Bio3D</description> |
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0
f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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3 <macros> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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4 <import>macros.xml</import> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
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5 </macros> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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changeset
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6 <expand macro="requirements" /> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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7 <command detect_errors="exit_code"> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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8 <![CDATA[ |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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9 Rscript '$__tool_directory__/pca.R' |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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changeset
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10 '$dcdin' |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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11 '$pdbin' |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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12 '$method' |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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13 #if $pca.sele == 'calpha': |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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14 "string" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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15 "calpha" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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16 #end if |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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17 #if $pca.sele == 'cbeta': |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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18 "string" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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19 '$pca.cbeta' |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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20 #end if |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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21 #if $pca.sele == 'backbone': |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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22 "string" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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23 "backbone" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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24 #end if |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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25 #if $pca.sele == 'sidechain': |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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26 "string" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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27 "sidechain" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
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28 #end if |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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29 #if $pca.sele == 'protein': |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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30 "string" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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31 "protein" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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32 #end if |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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changeset
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33 #if $pca.sele == 'ligand': |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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34 "string" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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35 "ligand" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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36 #end if |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
changeset
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37 #if $pca.sele == 'nucleic': |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
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38 "string" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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39 "nucleic" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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40 #end if |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
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41 #if $pca.sele == 'elety': |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
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42 "elety" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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43 '$pca.elety' |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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44 #end if |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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45 #if $pca.sele == 'resid': |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
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46 "resid" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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47 '$pca.resid' |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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48 #end if |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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49 #if $pca.sele == 'segid': |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
parents:
diff
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50 "segid" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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51 '$pca.segid' |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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52 #end if |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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53 '$output' |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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54 '$pca_plot' |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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55 '$pca_cluster' |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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56 '$pc1_rmsf' |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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57 2>&1 |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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58 ]]></command> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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59 <inputs> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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60 <expand macro="analysis_inputs"/> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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61 <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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62 label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" /> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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63 <conditional name="pca"> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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64 <param name="sele" type="select" label="Select domains"> |
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5
24867ab16f36
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
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65 <option value="calpha">C-alpha</option> |
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24867ab16f36
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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66 <option value="cbeta">C-beta</option> |
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0
f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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67 <option value="backbone">Backbone</option> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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68 <option value="sidechain">Sidechain</option> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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69 <option value="protein">Protein</option> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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70 <option value="ligand">Ligand</option> |
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5
24867ab16f36
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
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71 <option value="nucleic">Nucleic acids</option> |
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24867ab16f36
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
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72 <option value="elety">Atom names</option> |
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24867ab16f36
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
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73 <option value="resid">Residue ID</option> |
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24867ab16f36
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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74 <option value="segid">Segment ID</option> |
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0
f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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75 </param> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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76 <when value="calpha"> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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77 </when> |
|
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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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78 <when value="cbeta"> |
|
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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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79 </when> |
|
f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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80 <when value="backbone"> |
|
f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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81 </when> |
|
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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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82 <when value="sidechain"> |
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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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83 </when> |
|
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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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84 <when value="protein"> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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85 </when> |
|
f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
chemteam
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86 <when value="ligand"> |
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f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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87 </when> |
|
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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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88 <when value="nucleic"> |
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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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89 </when> |
|
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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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90 <when value="elety"> |
|
5
24867ab16f36
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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91 <param name="elety" type="text" value="CA" label="Atom name"/> |
|
0
f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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92 </when> |
|
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93 <when value="resid"> |
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5
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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94 <param name="resid" type="text" value="BGLC" label="Residue ID"/> |
|
0
f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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95 </when> |
|
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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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96 <when value="segid"> |
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5
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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97 <param name="segid" type="text" value="SUBS" label="Segment ID"/> |
|
0
f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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98 </when> |
|
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99 </conditional> |
|
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100 </inputs> |
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101 <outputs> |
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102 <data format="tabular" name="output" label="PCA raw data"/> |
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103 <data format="png" name="pca_plot" label="PCA plot"/> |
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104 <data format="png" name="pca_cluster" label="PCA Cluster Plot"/> |
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105 <data format="png" name="pc1_rmsf" label="PC1 on RMSF"/> |
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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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106 </outputs> |
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107 <tests> |
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108 <test> |
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109 <expand macro="tests_inputs"/> |
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110 <param name="method" value="false"/> |
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111 <param name="sele" value="calpha"/> |
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112 <output name="output"> |
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113 <assert_contents> |
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114 <has_n_columns n="4" /> |
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1
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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 8e1fece3eaef36823e90f5d10f8bb8b809544c55
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115 <has_line_matching expression="1\s+0.047.*\s+0.0374.*\s+0.0436.*" /> |
|
0
f56fb2762abb
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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116 </assert_contents> |
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117 </output> |
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118 </test> |
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119 </tests> |
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120 <help><![CDATA[ |
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121 .. class:: infomark |
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122 |
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123 **What it does** |
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124 |
|
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125 Principal component analysis (PCA) can be used to determine the relationship between statistically meaningful conformations (major global motions) |
|
0
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126 sampled during the trajectory. |
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127 |
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128 _____ |
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129 |
|
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130 |
|
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131 .. class:: infomark |
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132 |
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133 **Input** |
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134 |
|
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135 - Input file in PDB format |
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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136 - Input file in DCD format |
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0
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137 |
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138 _____ |
|
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139 |
|
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140 |
|
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141 .. class:: infomark |
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142 |
|
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143 **Output** |
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144 |
|
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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145 - Image (as PNG) of the PCA plot |
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24867ab16f36
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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146 - Image (as PNG) of the PCA clustered plot |
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24867ab16f36
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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147 - Image (as PNG) of the first principal component plotted on RMSF |
|
0
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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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148 - Tab-separated file of raw data |
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149 |
|
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150 ]]></help> |
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151 <expand macro="citations" /> |
|
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152 </tool> |