Mercurial > repos > iuc > snipit
annotate snipit.xml @ 1:9f23fe0cb70b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
author | iuc |
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date | Fri, 28 Oct 2022 20:58:45 +0000 |
parents | 20b4c59bec12 |
children | 92b9fd5f1f9f |
rev | line source |
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0
20b4c59bec12
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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1 <tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy0"> |
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
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diff
changeset
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2 <description>Summarise snps relative to a reference sequence</description> |
20b4c59bec12
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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3 <macros> |
1
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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0
diff
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4 <token name="@TOOL_VERSION@">1.0.7</token> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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5 <xml name="handle_background" tokens="format"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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0
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changeset
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6 <when value="@FORMAT@"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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7 <param argument="--solid-background" name="transparent_background" type="boolean" truevalue="" falsevalue="--solid-background" label="Plot on transparent background?" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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8 </when> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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0
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9 </xml> |
0
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
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diff
changeset
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10 </macros> |
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
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diff
changeset
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11 <requirements> |
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
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changeset
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12 <requirement type="package" version="@TOOL_VERSION@">snipit</requirement> |
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
diff
changeset
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13 </requirements> |
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
diff
changeset
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14 <command detect_errors="exit_code"><![CDATA[ |
1
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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0
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15 MPLCONFIGDIR=.matplotlib snipit '$alignment' |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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0
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changeset
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16 #if str($ref.select) == 'by_id' |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
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17 -r '$ref.id' |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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18 #end if |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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19 #if str($style.labels.choose) |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
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changeset
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20 -l '$style.labels.source' |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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21 #if str($style.labels.choose) == 'custom_csv' |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
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22 --l-header '${style.labels.names_column},${style.labels.labels_column}' |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
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23 #end if |
0
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
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diff
changeset
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24 #end if |
1
9f23fe0cb70b
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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25 -f $plot.format |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
changeset
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26 #if str($plot.format) in ['png', 'svg', 'tiff'] |
9f23fe0cb70b
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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27 $plot.transparent_background |
9f23fe0cb70b
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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28 #end if |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
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29 $write_snps |
9f23fe0cb70b
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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30 #if $dims.height > 0 |
9f23fe0cb70b
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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31 --height $dims.height |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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0
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32 #end if |
9f23fe0cb70b
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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33 #if $dims.width > 0 |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
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34 --width $dims.width |
0
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
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diff
changeset
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35 #end if |
1
9f23fe0cb70b
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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36 $dims.size_option |
9f23fe0cb70b
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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37 $style.flip_vertical |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
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38 #if len($pos_restrict.include_positions) |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
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39 --include-positions |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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40 #for $p in $pos_restrict.include_positions |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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41 '$p.pos' |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
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42 #end for |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
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43 #end if |
9f23fe0cb70b
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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44 #if len($pos_restrict.exclude_positions) |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
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45 --exclude-positions |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
diff
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46 #for $p in $pos_restrict.exclude_positions |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
0
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47 '$p.pos' |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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48 #end for |
0
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
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49 #end if |
1
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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50 $pos_restrict.exclude_ambig_pos |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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51 $style.sort.order |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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52 #if str($style.sort.order) == '--sort-by-mutation-number' |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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53 $style.sort.high_to_low |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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54 #else if str($style.sort.order) == '--sort-by-mutations' |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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55 #echo ','.join([str(p['pos']) for p in $style.sort.positions]) |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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56 $style.sort.high_to_low |
0
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
diff
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57 #end if |
1
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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58 #if not str($style.colouring.palette) |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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59 --recombi-mode --recombi-references '$style.colouring.parent1,$style.colouring.parent2' |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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60 #else |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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61 -c $style.colouring.palette |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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62 #end if |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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63 ]]></command> |
0
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
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64 <inputs> |
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
parents:
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65 <param name="alignment" format="fasta" type="data" label="Input alignment fasta file" /> |
1
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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66 <conditional name="ref"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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67 <param name="select" type="select" label="The reference sequence ..."> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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68 <option value="first">is the first sequence in the input</option> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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69 <option value="by_id">should be picked via its ID</option> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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70 </param> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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71 <when value="first" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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72 <when value="by_id"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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73 <param name="id" argument="--reference" type="text" label="ID of reference sequence" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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74 </when> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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75 </conditional> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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76 <section name="pos_restrict" title="Restrict genome positions to be plotted" expanded="false"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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77 <repeat name='include_positions' title="Restrict plot to specific regions/positions" min="0" default="0"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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78 <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'"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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79 <validator type="regex" message="Either a single position, e.g. 8347, or an interval like 8000-8500 is required">[0-9]+(-[0-9]+)*$</validator> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents:
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80 </param> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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81 </repeat> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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82 <repeat name='exclude_positions' title="Exclude specific regions/positions from plot" min="0" default="0"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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83 <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'."> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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84 <validator type="regex" message="Either a single position, e.g. 8347, or an interval like 8000-8500 is required">[0-9]+(-[0-9]+)*$</validator> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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85 </param> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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86 </repeat> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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87 <param argument="--exclude-ambig-pos" type="boolean" truevalue="--exclude-ambig-pos" falsevalue="" label="Exclude ambig positions?" help="Exclude positions with an ambiguous base in any sequences; considered after '--include-positions'." /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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88 </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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89 <section name="style" title="Customize rendering of samples and mutations" expanded="true"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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90 <conditional name="labels"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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91 <param name="choose" argument="-l" type="select" label="Provide custom labels for sequences?"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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92 <option value="">No, just use the sequence identifiers as labels in the plot</option> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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93 <option value="simple_csv">Yes, via a simple CSV dataset mapping names to labels</option> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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94 <option value="custom_csv">Yes, via a custom CSV dataset with column specification</option> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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95 </param> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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96 <when value="" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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97 <when value="simple_csv"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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98 <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." /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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99 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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100 <when value="custom_csv"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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101 <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." /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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102 <param name="names_column" type="text" label="Name of the sequence ID column" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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103 <param name="labels_column" type="text" label="Name of the column with desired labels" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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104 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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105 </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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106 <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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107 <param name="palette" type="select" value="classic" label="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)."> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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108 <option value="primary">primary</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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109 <option value="classic" selected="true">classic</option> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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110 <option value="purine-pyrimidine">purine-pyrimidine</option> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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111 <option value="greyscale">greyscale</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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112 <option value="wes">wes</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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113 <option value="verity">verity</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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114 <option value="">recombinant mutations colouring</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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115 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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116 <when value="primary" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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117 <when value="classic" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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118 <when value="purine-pyrimidine" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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119 <when value="greyscale" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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120 <when value="wes" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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121 <when 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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122 <when value=""> |
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123 <param name="parent1" type="text" label="Sequence ID of first recombinant parent sequence in alignment" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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124 <param name="parent2" type="text" label="Sequence ID of second recombinant parent sequence in alignment" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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125 </when> |
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126 </conditional> |
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127 <conditional name="sort"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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128 <param name="order" type="select" label="Order of samples in the plot"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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129 <option value="">Go with default</option> |
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130 <option value="--sort-by-id">Sort by sequence ID/label</option> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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131 <option value="--sort-by-mutation-number">Sort by number of mutations</option> |
9f23fe0cb70b
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132 <option value="--sort-by-mutations">Sort by bases at specified positions</option> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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133 </param> |
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134 <when value="" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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135 <when value="--sort-by-id" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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136 <when value="--sort-by-mutation-number"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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137 <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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138 </when> |
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139 <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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140 <repeat name="positions" title="Sort on" min="1" default="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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141 <param name="pos" type="integer" min="1" value="1" label="Sort (alphabetically) by base at position" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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142 </repeat> |
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143 <param argument="--high-to-low" type="boolean" truevalue="--high-to-low" falsevalue="" label="Invert resulting sort order" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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144 </when> |
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145 </conditional> |
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146 <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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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147 </section> |
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148 <conditional name="plot"> |
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149 <param argument="--format" type="select" value="png" label="Plot output file format"> |
0
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150 <option value="png" selected="true">png</option> |
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151 <option value="jpg">jpg</option> |
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152 <option value="pdf">pdf</option> |
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153 <option value="svg">svg</option> |
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154 <option value="tiff">tiff</option> |
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155 </param> |
1
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156 <when value="jpg" /> |
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157 <when 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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158 <expand macro="handle_background" format="png" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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159 <expand macro="handle_background" format="svg" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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160 <expand macro="handle_background" format="tiff" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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161 </conditional> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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162 <section name="dims" title="Customize plot dimensions" expanded="false"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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163 <param argument="--width" type="float" value="0" min="0" label="Figure width" help="Set to 0 to keep default figure width." /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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164 <param argument="--height" type="float" value="0" min="0" label="Figure height" help="Set to 0 to keep default figure height." /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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165 <param argument="--size-option" type="select" value="scale" label="Plot sizing options"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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166 <option value="--size-option expand">expand</option> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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167 <option value="" selected="true">scale</option> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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168 </param> |
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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169 </section> |
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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170 <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." /> |
0
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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171 </inputs> |
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172 <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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173 <data name="snp_plot" format="png" label="snipit on ${on_string}: Plot" from_work_dir="snp_plot.*"> |
0
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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174 <change_format> |
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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175 <when input="plot.format" value="jpg" format="jpg" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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176 <when input="plot.format" value="pdf" format="pdf" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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177 <when input="plot.format" value="svg" format="svg" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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178 <when input="plot.format" value="tiff" format="tiff" /> |
0
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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179 </change_format> |
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180 </data> |
1
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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181 <data name="snps" format="csv" label="snipit on ${on_string}: SNPs" from_work_dir="snps.csv"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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182 <filter>write_snps</filter> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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183 <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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184 <action name="column_names" type="metadata" default="record,snps,num_snps" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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185 </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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186 </data> |
0
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187 </outputs> |
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188 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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189 <test expect_num_outputs="2"> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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190 <param name="alignment" value="input.fasta" /> |
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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191 <param name="write_snps" 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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192 <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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193 <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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194 </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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195 <output name="snp_plot" ftype="png" file="snp_plot.png" compare="sim_size" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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196 <output name="snps" ftype="csv" file="snps.csv" /> |
0
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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197 </test> |
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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198 <test expect_num_outputs="1"> |
0
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199 <param name="alignment" value="input.fasta" /> |
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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200 <conditional name="ref"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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201 <param name="select" value="by_id" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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202 <param name="id" value="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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203 </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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204 <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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205 <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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206 </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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207 <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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208 <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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209 </conditional> |
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210 <assert_command> |
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211 <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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212 <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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213 </assert_command> |
0
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214 <output name="snp_plot" ftype="pdf" file="snp_plot.pdf" compare="sim_size" /> |
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215 </test> |
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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216 <test expect_num_outputs="1"> |
0
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217 <param name="alignment" value="input.fasta" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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218 <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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219 <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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220 <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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221 </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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222 </section> |
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223 <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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224 <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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225 <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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226 </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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227 <output name="snp_plot" ftype="jpg" file="snp_plot.jpg" compare="sim_size" /> |
0
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228 </test> |
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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229 <test expect_num_outputs="1"> |
0
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230 <param name="alignment" value="input.fasta" /> |
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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 <section name="pos_restrict"> |
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232 <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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233 <param name="pos" value="1-10000" /> |
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234 </repeat> |
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235 <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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236 <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
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237 </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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238 <repeat name="exclude_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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239 <param name="pos" value="1000-2000" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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240 </repeat> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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241 <param name="exclude_ambig_pos" value="true" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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242 </section> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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243 <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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244 <conditional name="sort"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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245 <param name="order" value="--sort-by-mutations" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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246 <repeat name="positions"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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247 <param name="pos" value="3" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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248 </repeat> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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249 <repeat name="positions"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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250 <param name="pos" value="1" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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251 </repeat> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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252 <repeat name="positions"> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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253 <param name="pos" value="2" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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254 </repeat> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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255 <param name="high_to_low" value="true" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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256 </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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257 </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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258 <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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259 <param name="format" value="svg" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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260 <param name="transparent_background" value="true" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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261 </conditional> |
9f23fe0cb70b
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="--include-positions '1-10000' '10001-30000'" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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264 <has_text text="--exclude-positions '1000-2000'" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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265 <has_text text="--exclude-ambig-pos" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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266 <has_text text="--sort-by-mutations 3,1,2" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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267 <has_text text="--high-to-low" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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268 </assert_command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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269 <output name="snp_plot" ftype="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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270 <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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271 <!-- check that the plot does NOT refer to excluded |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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272 position 1059, uses darkseagreen (to highlight Ts) and |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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273 transparent (i.e. NOT white) background --> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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274 <not_has_text text="<!-- 1059 -->" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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275 <has_text text="style="fill: #8fbc8f" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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276 <not_has_text text="style="fill: #ffffff"" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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277 </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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278 </output> |
0
20b4c59bec12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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279 </test> |
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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280 <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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281 <param name="alignment" value="input.fasta" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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282 <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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283 <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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284 <param name="palette" value="" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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285 <param name="parent1" value="USA_1" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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286 <param name="parent2" value="USA_5" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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287 </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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288 </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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289 <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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290 <param name="format" value="svg" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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291 </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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292 <output name="snp_plot" ftype="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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293 <assert_contents> |
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294 <!-- check that the plot does mention position 1059, |
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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 uses goldenrod and #EA5463 as colors (to |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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296 indicate private and parent2 mutations, respectively, in |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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297 recombi-mode) and uses a solid white background --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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298 <has_text text="<!-- 1059 -->" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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299 <has_text text="style="fill: #daa520" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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300 <has_text text="style="fill: #ea5463" /> |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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301 <has_text text="style="fill: #ffffff"" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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302 </assert_contents> |
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303 </output> |
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304 </test> |
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305 <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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306 <param name="alignment" value="input.fasta" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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307 <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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308 <conditional name="labels"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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309 <param name="choose" value="custom_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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310 <param name="source" value="custom_labels.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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311 <param name="names_column" value="ori" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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312 <param name="labels_column" value="new" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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313 </conditional> |
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314 </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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315 <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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316 <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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317 </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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318 <output name="snp_plot" ftype="svg"> |
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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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319 <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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320 <!-- check that the plot does not mention the original |
9f23fe0cb70b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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321 seq IDs but the mapped labels --> |
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322 <not_has_text text="USA_" /> |
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323 <has_text text="SAMPLE_" /> |
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324 </assert_contents> |
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325 </output> |
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326 </test> |
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327 |
0
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328 </tests> |
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329 <help><![CDATA[ |
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330 **What it does** |
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331 |
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332 Snipit finds the SNPs relative to a reference in a multiple sequence alignment and highlights these changes as a figure. |
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333 ]]> |
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334 </help> |
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335 <citations> |
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336 <citation type="bibtex"> |
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337 @UNPUBLISHED{OToole2017, |
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338 author = {O'Toole, Aine}, |
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339 title = {snipit: Summarise snps relative to your reference sequence.}, |
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340 year = {2017}, |
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341 url = {https://github.com/aineniamh/snipit} |
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342 } |
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343 </citation> |
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344 </citations> |
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345 </tool> |