Mercurial > repos > iuc > snipit
annotate snipit.xml @ 2:9e12d66c47f4 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
| author | iuc |
|---|---|
| date | Sat, 16 Nov 2024 11:07:34 +0000 |
| parents | f0b0037669e9 |
| children |
| rev | line source |
|---|---|
|
2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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1 <tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1"> |
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0
a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
diff
changeset
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2 <description>Summarise snps relative to a reference sequence</description> |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
diff
changeset
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3 <macros> |
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2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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4 <token name="@TOOL_VERSION@">1.6</token> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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5 <token name="@VERSION_SUFFIX@">0</token> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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6 <xml name="ref_select" token_help=""> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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7 <conditional name="ref"> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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8 <param name="select" type="select" label="The reference sequence ..." |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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9 help="@HELP@"> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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10 <option value="first">is the first sequence in the input</option> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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11 <option value="by_id">should be picked via its ID</option> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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12 </param> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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13 <when value="first" /> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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14 <when value="by_id"> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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15 <param name="id" argument="--reference" type="text" label="ID of reference sequence" /> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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16 </when> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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17 </conditional> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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18 </xml> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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19 <xml name="handle_background" tokens="format"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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20 <when value="@FORMAT@"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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21 <param argument="--solid-background" name="transparent_background" type="boolean" truevalue="" falsevalue="--solid-background" label="Plot on transparent background?" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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22 </when> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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23 </xml> |
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0
a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
diff
changeset
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24 </macros> |
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2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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25 <xrefs> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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26 <xref type="bio.tools">snipit</xref> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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27 </xrefs> |
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0
a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
diff
changeset
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28 <requirements> |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
diff
changeset
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29 <requirement type="package" version="@TOOL_VERSION@">snipit</requirement> |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
diff
changeset
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30 </requirements> |
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2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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31 <version_command>snipit -v</version_command> |
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0
a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
diff
changeset
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32 <command detect_errors="exit_code"><![CDATA[ |
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2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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33 snipit '$alignment' |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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34 --sequence-type $mode.sequence_type |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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35 ## --cds-mode flag broken in this version of snipit |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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36 ## but this is how it'd be used. |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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37 ##if str($mode.sequence_type) == 'nt' |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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38 ## $mode.cds_mode |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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39 ##end if |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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40 #if str($mode.ref.select) == 'by_id' |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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41 -r '$ref.id' |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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42 #end if |
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2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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43 #if not str($mode.colouring.palette) |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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44 --recombi-mode --recombi-references '$mode.colouring.parent1,$mode.colouring.parent2' |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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45 #else |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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46 -c $mode.colouring.palette |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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47 #end if |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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48 $pos_restrict.show_indels |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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49 --ambig-mode $pos_restrict.ambig_mode |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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50 #if len($pos_restrict.include_positions) |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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51 --include-positions |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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52 #for $p in $pos_restrict.include_positions |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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53 '$p.pos' |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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54 #end for |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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55 #end if |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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56 #if len($pos_restrict.exclude_positions) |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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57 --exclude-positions |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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58 #for $p in $pos_restrict.exclude_positions |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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59 '$p.pos' |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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60 #end for |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
1
diff
changeset
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61 #end if |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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62 #if str($style.labels.choose) |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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63 -l '$style.labels.source' |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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diff
changeset
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64 #if str($style.labels.choose) == 'custom_csv' |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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65 --l-header '${style.labels.names_column},${style.labels.labels_column}' |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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66 #end if |
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0
a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
diff
changeset
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67 #end if |
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2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
parents:
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68 $style.position_labels |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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diff
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69 -f $plot.format |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
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70 #if str($plot.format) in ['png', 'svg', 'tiff'] |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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71 $plot.transparent_background |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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diff
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72 #end if |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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diff
changeset
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73 $write_snps |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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diff
changeset
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74 #if $dims.height > 0 |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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75 --height $dims.height |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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76 #end if |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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77 #if $dims.width > 0 |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
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78 --width $dims.width |
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0
a9f156e31071
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79 #end if |
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80 $dims.size_option |
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81 $style.flip_vertical |
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82 $style.sort.order |
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83 #if str($style.sort.order) == '--sort-by-mutation-number' |
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84 $style.sort.high_to_low |
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85 #else if str($style.sort.order) == '--sort-by-mutations' |
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86 #echo ','.join([str(p['pos']) for p in $style.sort.positions]) |
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87 $style.sort.high_to_low |
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88 #end if |
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89 ]]></command> |
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90 <environment_variables> |
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91 <environment_variable name="MPLCONFIGDIR">.matplotlib</environment_variable> |
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92 </environment_variables> |
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93 <inputs> |
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94 <param name="alignment" format="fasta" type="data" label="Input alignment fasta file" /> |
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95 <conditional name="mode"> |
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96 <param argument="--sequence-type" type="select" label="Type of input"> |
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97 <option value="nt">DNA sequence alignment</option> |
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98 <option value="aa">Protein sequence alignment</option> |
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99 </param> |
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100 <when value="nt"> |
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101 <expand macro="ref_select" help="Please note that you will HAVE to specify the reference explicitly via its ID if you choose the 'recombinant mutations colouring' scheme and in this case the reference can NOT be one of the recombinant parents." /> |
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102 <!-- cds-mode flag is broken in this version of snipit |
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103 so not enabling the param for now. |
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104 When enabling remember to fix the double dashes! |
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105 <param argument="- -cds-mode" type="boolean" truevalue="- -cds-mode" falsevalue="" label="Perform coding sequence alignment check?" help="By selecting this option you are indicating that your input is an alignment of coding sequences. The tool will check that all sequence lengths are multiples of three and will fail if that is not the case." /> |
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106 --> |
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107 <conditional name="colouring"> |
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108 <param name="palette" argument="--colour-palette" type="select" label="Plotted Mutations colouring scheme" help="Mutations can be coloured by base change or, alternatively, by their presence/absence in any of two parent sequences in the alignment (recombinant mode)."> |
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109 <option value="primary">primary</option> |
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110 <option value="classic" selected="true">classic</option> |
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111 <option value="classic_extended">classic_extended (only scheme defining colours for ambiguous bases)</option> |
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112 <option value="purine-pyrimidine">purine-pyrimidine</option> |
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113 <option value="greyscale">greyscale</option> |
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114 <option value="wes">wes</option> |
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115 <option value="verity">verity</option> |
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116 <option value="">recombinant mutations colouring</option> |
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117 </param> |
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118 <when value="primary" /> |
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119 <when value="classic" /> |
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120 <when value="classic_extended" /> |
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121 <when value="purine-pyrimidine" /> |
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122 <when value="greyscale" /> |
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123 <when value="wes" /> |
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124 <when value="verity" /> |
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125 <when value=""> |
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126 <param name="parent1" type="text" label="Sequence ID of first recombinant parent sequence in alignment" /> |
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127 <param name="parent2" type="text" label="Sequence ID of second recombinant parent sequence in alignment" /> |
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128 </when> |
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129 </conditional> |
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130 </when> |
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131 <when value="aa"> |
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132 <expand macro="ref_select" /> |
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133 <conditional name="colouring"> |
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134 <param name="palette" argument="--colour-palette" type="select" label="Plotted Mutations colouring scheme" help="The only currently available colour scheme for protein sequences is 'ugene', which defines colours for the 20 AAs and all AA ambiguity symbols."> |
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135 <option value="ugene">ugene</option> |
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136 </param> |
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137 <when value="ugene" /> |
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138 </conditional> |
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1
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139 </when> |
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140 </conditional> |
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2
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141 <section name="pos_restrict" title="Restrict alignment positions to be plotted" expanded="true"> |
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142 <param argument="--show-indels" type="boolean" truevalue="--show-indels" falsevalue="" label="Include insertion and deletion mutations" /> |
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143 <param argument="--ambig-mode" type="select" label="Plotting of positions with ambiguity symbols"> |
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144 <option value="all">Treat ambiguity symbols like mutations; plot all such positions (all)</option> |
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145 <option value="snps" selected="true">Show ambiguity symbols for positions with mutations in other sequences (snps)</option> |
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146 <option value="exclude">Never plot positions that involve ambiguous symbols (exclude)</option> |
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147 </param> |
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148 <repeat name="include_positions" title="Restrict plot to specific regions/positions" min="0" default="0"> |
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1
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149 <param argument="--include-positions" name="pos" type="text" label="Include position/region" help="A range (closed, inclusive; one-indexed) or specific position to include in the output, e.g. '100-150' or '100'"> |
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150 <validator type="regex" message="Either a single position, e.g. 8347, or an interval like 8000-8500 is required">[0-9]+(-[0-9]+)*$</validator> |
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151 </param> |
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152 </repeat> |
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153 <repeat name='exclude_positions' title="Exclude specific regions/positions from plot" min="0" default="0"> |
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154 <param argument="--exclude-positions" name="pos" type="text" label="Exclude position/region" help="A range (closed, inclusive; one-indexed) or specific position to exclude from the output, e.g. '100-150' or '100'; considered after any '--include-positions'."> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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155 <validator type="regex" message="Either a single position, e.g. 8347, or an interval like 8000-8500 is required">[0-9]+(-[0-9]+)*$</validator> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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156 </param> |
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157 </repeat> |
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158 </section> |
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159 <section name="style" title="Customize rendering of samples and mutations" expanded="true"> |
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160 <conditional name="labels"> |
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161 <param name="choose" argument="-l" type="select" label="Provide custom labels for sequences?"> |
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162 <option value="">No, just use the sequence identifiers as labels in the plot</option> |
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163 <option value="simple_csv">Yes, via a simple CSV dataset mapping names to labels</option> |
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164 <option value="custom_csv">Yes, via a custom CSV dataset with column specification</option> |
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165 </param> |
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166 <when value="" /> |
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167 <when value="simple_csv"> |
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168 <param argument="--labels" name="source" type="data" format="csv" label="Labels mapping source" help="This expects a CSV dataset with two columns named 'name' and 'label' where the values in the 'name' column must have matches for all sequence IDs (including the reference) in the alignment input." /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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169 </when> |
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170 <when value="custom_csv"> |
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171 <param argument="--labels" name="source" type="data" format="csv" label="Labels mapping source" help="Select a CSV dataset with an arbitrary number of named columns here and specify below which column contains the sequence IDs to be mapped and which one the labels to be used instead. The dataset must define mappings for all sequence IDs including the reference." /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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172 <param name="names_column" type="text" label="Name of the sequence ID column" /> |
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173 <param name="labels_column" type="text" label="Name of the column with desired labels" /> |
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174 </when> |
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175 </conditional> |
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2
9e12d66c47f4
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176 <param name="position_labels" type="boolean" truevalue="" falsevalue="--remove-site-text" checked="true" label="Label plotted sites with position" /> |
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177 <conditional name="sort"> |
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178 <param name="order" type="select" label="Order of samples in the plot"> |
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179 <option value="">Go with default</option> |
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180 <option value="--sort-by-id">Sort by sequence ID/label</option> |
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181 <option value="--sort-by-mutation-number">Sort by number of mutations</option> |
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182 <option value="--sort-by-mutations">Sort by bases at specified positions</option> |
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183 </param> |
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184 <when value="" /> |
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185 <when value="--sort-by-id" /> |
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186 <when value="--sort-by-mutation-number"> |
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187 <param argument="--high-to-low" type="boolean" truevalue="--high-to-low" falsevalue="" label="Invert sort order" help="If selected sort sequences from highest to lowest number of mutations instead of from lowest to highest." /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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188 </when> |
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189 <when value="--sort-by-mutations"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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190 <repeat name="positions" title="Sort on" min="1" default="1"> |
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191 <param name="pos" type="integer" min="1" value="1" label="Sort (alphabetically) by base at position" /> |
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192 </repeat> |
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193 <param argument="--high-to-low" type="boolean" truevalue="--high-to-low" falsevalue="" label="Invert resulting sort order" /> |
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194 </when> |
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195 </conditional> |
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196 <param argument="--flip-vertical" type="boolean" truevalue="--flip-vertical" falsevalue="" label="Flip plot orientation?" help="Flip the orientation of the plot so sequences are below the reference rather than above it." /> |
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197 </section> |
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198 <conditional name="plot"> |
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199 <param argument="--format" type="select" value="png" label="Plot output file format"> |
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200 <option value="png" selected="true">png</option> |
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201 <option value="jpg">jpg</option> |
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202 <option value="pdf">pdf</option> |
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203 <option value="svg">svg</option> |
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204 <option value="tiff">tiff</option> |
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205 </param> |
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1
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206 <when value="jpg" /> |
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207 <when value="pdf" /> |
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208 <expand macro="handle_background" format="png" /> |
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209 <expand macro="handle_background" format="svg" /> |
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210 <expand macro="handle_background" format="tiff" /> |
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211 </conditional> |
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212 <section name="dims" title="Customize plot dimensions" expanded="false"> |
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213 <param argument="--width" type="float" value="0" min="0" label="Figure width" help="Set to 0 to keep default figure width." /> |
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214 <param argument="--height" type="float" value="0" min="0" label="Figure height" help="Set to 0 to keep default figure height." /> |
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215 <param argument="--size-option" type="select" value="scale" label="Plot sizing options"> |
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216 <option value="--size-option expand">expand</option> |
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217 <option value="" selected="true">scale</option> |
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218 </param> |
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219 </section> |
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1
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220 <param argument="--write-snps" type="boolean" truevalue="-s" falsevalue="" label="Write out SNPs?" help="Produces extra CSV output with lists of SNPs per sequence in the alignment if enabled." /> |
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221 </inputs> |
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222 <outputs> |
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223 <data name="snp_plot" format="png" label="snipit on ${on_string}: Plot" from_work_dir="snp_plot.*"> |
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0
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224 <change_format> |
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1
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225 <when input="plot.format" value="jpg" format="jpg" /> |
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226 <when input="plot.format" value="pdf" format="pdf" /> |
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227 <when input="plot.format" value="svg" format="svg" /> |
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228 <when input="plot.format" value="tiff" format="tiff" /> |
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229 </change_format> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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230 </data> |
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1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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231 <data name="snps" format="csv" label="snipit on ${on_string}: SNPs" from_work_dir="snps.csv"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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232 <filter>write_snps</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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233 <actions> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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234 <action name="column_names" type="metadata" default="record,snps,num_snps" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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235 </actions> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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236 </data> |
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0
a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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237 </outputs> |
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238 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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239 <test expect_num_outputs="2"> |
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0
a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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240 <param name="alignment" value="input.fasta" /> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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241 <param name="write_snps" value="true" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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242 <conditional name="plot"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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243 <param name="transparent_background" value="true" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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244 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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245 <output name="snp_plot" ftype="png" file="snp_plot.png" compare="sim_size" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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246 <output name="snps" ftype="csv" file="snps.csv" /> |
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0
a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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247 </test> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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248 <test expect_num_outputs="1"> |
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0
a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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249 <param name="alignment" value="input.fasta" /> |
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2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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250 <conditional name="mode"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
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251 <conditional name="ref"> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
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252 <param name="select" value="by_id" /> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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253 <param name="id" value="USA_2" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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254 </conditional> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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255 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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256 <section name="style"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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257 <param name="flip_vertical" value="true" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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258 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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259 <conditional name="plot"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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260 <param name="format" value="pdf" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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261 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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262 <assert_command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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263 <has_text text="-r 'USA_2'" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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264 <has_text text="--flip-vertical" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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265 </assert_command> |
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266 <output name="snp_plot" ftype="pdf" file="snp_plot.pdf" compare="sim_size" /> |
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267 </test> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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268 <test expect_num_outputs="1"> |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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269 <param name="alignment" value="input.fasta" /> |
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2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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270 <conditional name="mode"> |
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1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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271 <conditional name="colouring"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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272 <param name="palette" value="verity" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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273 </conditional> |
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2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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274 </conditional> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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275 <conditional name="plot"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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276 <param name="format" value="jpg" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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277 <param name="transparent_background" value="true" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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278 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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279 <output name="snp_plot" ftype="jpg" file="snp_plot.jpg" compare="sim_size" /> |
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0
a9f156e31071
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280 </test> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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281 <test expect_num_outputs="1"> |
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a9f156e31071
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282 <param name="alignment" value="input.fasta" /> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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283 <section name="pos_restrict"> |
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2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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284 <param name="ambig_mode" value="exclude" /> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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285 <repeat name="include_positions"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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286 <param name="pos" value="1-10000" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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287 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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288 <repeat name="include_positions"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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289 <param name="pos" value="10001-30000" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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290 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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291 <repeat name="exclude_positions"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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292 <param name="pos" value="1000-2000" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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293 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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294 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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295 <section name="style"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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296 <conditional name="sort"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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297 <param name="order" value="--sort-by-mutations" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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298 <repeat name="positions"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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299 <param name="pos" value="3" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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300 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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301 <repeat name="positions"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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302 <param name="pos" value="1" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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303 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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304 <repeat name="positions"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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305 <param name="pos" value="2" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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306 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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307 <param name="high_to_low" value="true" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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308 </conditional> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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309 </section> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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310 <conditional name="plot"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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311 <param name="format" value="svg" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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312 <param name="transparent_background" value="true" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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313 </conditional> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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314 <assert_command> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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315 <has_text text="--include-positions '1-10000' '10001-30000'" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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316 <has_text text="--exclude-positions '1000-2000'" /> |
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2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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317 <has_text text="--ambig-mode exclude" /> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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318 <has_text text="--sort-by-mutations 3,1,2" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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319 <has_text text="--high-to-low" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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320 </assert_command> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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321 <output name="snp_plot" ftype="svg"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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322 <assert_contents> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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323 <!-- check that the plot does NOT refer to excluded |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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324 position 1059, uses darkseagreen (to highlight Ts) and |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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325 transparent (i.e. NOT white) background --> |
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2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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326 <has_line_matching expression=".*<text .+>1059</text>" negate="true" /> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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327 <has_text text="style="fill: #8fbc8f" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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328 <not_has_text text="style="fill: #ffffff"" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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329 </assert_contents> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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330 </output> |
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a9f156e31071
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331 </test> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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332 <test expect_num_outputs="1"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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333 <param name="alignment" value="input.fasta" /> |
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2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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334 <conditional name="mode"> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
iuc
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335 <conditional name="ref"> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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336 <param name="select" value="by_id" /> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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337 <param name="id" value="reference" /> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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338 </conditional> |
|
1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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339 <conditional name="colouring"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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340 <param name="palette" value="" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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341 <param name="parent1" value="USA_1" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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342 <param name="parent2" value="USA_5" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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343 </conditional> |
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2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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344 </conditional> |
|
1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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345 <conditional name="plot"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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346 <param name="format" value="svg" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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347 </conditional> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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348 <output name="snp_plot" ftype="svg"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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349 <assert_contents> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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350 <!-- check that the plot does mention position 1059, |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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351 uses goldenrod and #EA5463 as colors (to |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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352 indicate private and parent2 mutations, respectively, in |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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353 recombi-mode) and uses a solid white background --> |
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9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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354 <has_line_matching expression=".*<text .+>1059</text>" /> |
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1
f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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355 <has_text text="style="fill: #daa520" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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356 <has_text text="style="fill: #ea5463" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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357 <has_text text="style="fill: #ffffff"" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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358 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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359 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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360 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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361 <test expect_num_outputs="1"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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362 <param name="alignment" value="input.fasta" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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363 <section name="style"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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364 <conditional name="labels"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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365 <param name="choose" value="custom_csv" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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366 <param name="source" value="custom_labels.csv" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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367 <param name="names_column" value="ori" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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368 <param name="labels_column" value="new" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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369 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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370 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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371 <conditional name="plot"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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372 <param name="format" value="svg" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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373 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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374 <output name="snp_plot" ftype="svg"> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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375 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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376 <!-- check that the plot does not mention the original |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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377 seq IDs but the mapped labels --> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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378 <not_has_text text="USA_" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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379 <has_text text="SAMPLE_" /> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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380 </assert_contents> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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381 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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382 </test> |
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f0b0037669e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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383 |
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0
a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
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changeset
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384 </tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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385 <help><![CDATA[ |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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386 **What it does** |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
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changeset
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387 |
|
2
9e12d66c47f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 64c7062a60708a60b5779fa3406aca8e07828d35
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388 Snipit finds mutations relative to a reference in a multiple sequence alignment and presents these changes in a nice overview plot. |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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389 ]]> |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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390 </help> |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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391 <citations> |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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392 <citation type="bibtex"> |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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393 @UNPUBLISHED{OToole2017, |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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394 author = {O'Toole, Aine}, |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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395 title = {snipit: Summarise snps relative to your reference sequence.}, |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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396 year = {2017}, |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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397 url = {https://github.com/aineniamh/snipit} |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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398 } |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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399 </citation> |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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400 </citations> |
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a9f156e31071
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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401 </tool> |