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annotate snipit.xml @ 1:f0b0037669e9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
author iuc
date Fri, 28 Oct 2022 20:58:00 +0000
parents a9f156e31071
children 9e12d66c47f4
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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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1 <tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy0">
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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2 <description>Summarise snps relative to a reference sequence</description>
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
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3 <macros>
1
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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4 <token name="@TOOL_VERSION@">1.0.7</token>
f0b0037669e9 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">
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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6 <when value="@FORMAT@">
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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7 <param argument="--solid-background" name="transparent_background" type="boolean" truevalue="" falsevalue="--solid-background" label="Plot on transparent background?" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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8 </when>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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9 </xml>
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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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10 </macros>
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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11 <requirements>
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
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12 <requirement type="package" version="@TOOL_VERSION@">snipit</requirement>
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
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13 </requirements>
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
iuc
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14 <command detect_errors="exit_code"><![CDATA[
1
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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15 MPLCONFIGDIR=.matplotlib snipit '$alignment'
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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16 #if str($ref.select) == 'by_id'
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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17 -r '$ref.id'
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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18 #end if
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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19 #if str($style.labels.choose)
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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20 -l '$style.labels.source'
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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21 #if str($style.labels.choose) == 'custom_csv'
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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22 --l-header '${style.labels.names_column},${style.labels.labels_column}'
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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23 #end if
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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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24 #end if
1
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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25 -f $plot.format
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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26 #if str($plot.format) in ['png', 'svg', 'tiff']
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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27 $plot.transparent_background
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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28 #end if
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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29 $write_snps
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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30 #if $dims.height > 0
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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31 --height $dims.height
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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32 #end if
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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33 #if $dims.width > 0
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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34 --width $dims.width
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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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35 #end if
1
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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36 $dims.size_option
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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37 $style.flip_vertical
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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38 #if len($pos_restrict.include_positions)
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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39 --include-positions
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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40 #for $p in $pos_restrict.include_positions
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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41 '$p.pos'
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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42 #end for
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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43 #end if
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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44 #if len($pos_restrict.exclude_positions)
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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45 --exclude-positions
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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46 #for $p in $pos_restrict.exclude_positions
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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47 '$p.pos'
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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48 #end for
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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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49 #end if
1
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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50 $pos_restrict.exclude_ambig_pos
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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51 $style.sort.order
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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52 #if str($style.sort.order) == '--sort-by-mutation-number'
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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53 $style.sort.high_to_low
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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54 #else if str($style.sort.order) == '--sort-by-mutations'
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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55 #echo ','.join([str(p['pos']) for p in $style.sort.positions])
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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56 $style.sort.high_to_low
0
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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57 #end if
1
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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58 #if not str($style.colouring.palette)
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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59 --recombi-mode --recombi-references '$style.colouring.parent1,$style.colouring.parent2'
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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60 #else
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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61 -c $style.colouring.palette
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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62 #end if
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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63 ]]></command>
0
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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64 <inputs>
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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65 <param name="alignment" format="fasta" type="data" label="Input alignment fasta file" />
1
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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66 <conditional name="ref">
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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67 <param name="select" type="select" label="The reference sequence ...">
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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68 <option value="first">is the first sequence in the input</option>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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69 <option value="by_id">should be picked via its ID</option>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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70 </param>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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71 <when value="first" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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72 <when value="by_id">
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73 <param name="id" argument="--reference" type="text" label="ID of reference sequence" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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74 </when>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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75 </conditional>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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76 <section name="pos_restrict" title="Restrict genome positions to be plotted" expanded="false">
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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77 <repeat name='include_positions' title="Restrict plot to specific regions/positions" min="0" default="0">
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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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'">
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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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>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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80 </param>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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81 </repeat>
f0b0037669e9 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">
f0b0037669e9 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'.">
f0b0037669e9 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>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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85 </param>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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86 </repeat>
f0b0037669e9 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'." />
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88 </section>
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89 <section name="style" title="Customize rendering of samples and mutations" expanded="true">
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90 <conditional name="labels">
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91 <param name="choose" argument="-l" type="select" label="Provide custom labels for sequences?">
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92 <option value="">No, just use the sequence identifiers as labels in the plot</option>
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93 <option value="simple_csv">Yes, via a simple CSV dataset mapping names to labels</option>
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94 <option value="custom_csv">Yes, via a custom CSV dataset with column specification</option>
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95 </param>
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96 <when value="" />
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97 <when value="simple_csv">
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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." />
f0b0037669e9 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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100 <when value="custom_csv">
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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." />
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102 <param name="names_column" type="text" label="Name of the sequence ID column" />
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103 <param name="labels_column" type="text" label="Name of the column with desired labels" />
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104 </when>
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105 </conditional>
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106 <conditional name="colouring">
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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).">
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108 <option value="primary">primary</option>
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109 <option value="classic" selected="true">classic</option>
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110 <option value="purine-pyrimidine">purine-pyrimidine</option>
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111 <option value="greyscale">greyscale</option>
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112 <option value="wes">wes</option>
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113 <option value="verity">verity</option>
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114 <option value="">recombinant mutations colouring</option>
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115 </param>
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116 <when value="primary" />
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117 <when value="classic" />
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118 <when value="purine-pyrimidine" />
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119 <when value="greyscale" />
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120 <when value="wes" />
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121 <when value="verity" />
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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" />
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124 <param name="parent2" type="text" label="Sequence ID of second recombinant parent sequence in alignment" />
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125 </when>
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126 </conditional>
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127 <conditional name="sort">
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128 <param name="order" type="select" label="Order of samples in the plot">
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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>
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131 <option value="--sort-by-mutation-number">Sort by number of mutations</option>
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132 <option value="--sort-by-mutations">Sort by bases at specified positions</option>
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133 </param>
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134 <when value="" />
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135 <when value="--sort-by-id" />
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136 <when value="--sort-by-mutation-number">
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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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138 </when>
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139 <when value="--sort-by-mutations">
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140 <repeat name="positions" title="Sort on" min="1" default="1">
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141 <param name="pos" type="integer" min="1" value="1" label="Sort (alphabetically) by base at position" />
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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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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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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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158 <expand macro="handle_background" format="png" />
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159 <expand macro="handle_background" format="svg" />
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160 <expand macro="handle_background" format="tiff" />
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161 </conditional>
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162 <section name="dims" title="Customize plot dimensions" expanded="false">
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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." />
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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." />
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165 <param argument="--size-option" type="select" value="scale" label="Plot sizing options">
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166 <option value="--size-option expand">expand</option>
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167 <option value="" selected="true">scale</option>
0
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168 </param>
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169 </section>
1
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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
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171 </inputs>
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172 <outputs>
1
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173 <data name="snp_plot" format="png" label="snipit on ${on_string}: Plot" from_work_dir="snp_plot.*">
0
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174 <change_format>
1
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175 <when input="plot.format" value="jpg" format="jpg" />
f0b0037669e9 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" />
f0b0037669e9 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" />
f0b0037669e9 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
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179 </change_format>
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180 </data>
1
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181 <data name="snps" format="csv" label="snipit on ${on_string}: SNPs" from_work_dir="snps.csv">
f0b0037669e9 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>
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183 <actions>
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184 <action name="column_names" type="metadata" default="record,snps,num_snps" />
f0b0037669e9 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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186 </data>
0
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187 </outputs>
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188 <tests>
1
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189 <test expect_num_outputs="2">
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190 <param name="alignment" value="input.fasta" />
1
f0b0037669e9 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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192 <conditional name="plot">
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193 <param name="transparent_background" value="true" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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194 </conditional>
f0b0037669e9 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" />
f0b0037669e9 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
a9f156e31071 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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198 <test expect_num_outputs="1">
0
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199 <param name="alignment" value="input.fasta" />
1
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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200 <conditional name="ref">
f0b0037669e9 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" />
f0b0037669e9 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" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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203 </conditional>
f0b0037669e9 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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iuc
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205 <param name="flip_vertical" value="true" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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206 </section>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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207 <conditional name="plot">
f0b0037669e9 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" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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209 </conditional>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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210 <assert_command>
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211 <has_text text="-r 'USA_2'" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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212 <has_text text="--flip-vertical" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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213 </assert_command>
0
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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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
f0b0037669e9 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
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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217 <param name="alignment" value="input.fasta" />
1
f0b0037669e9 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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219 <conditional name="colouring">
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220 <param name="palette" value="verity" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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221 </conditional>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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222 </section>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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223 <conditional name="plot">
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iuc
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224 <param name="format" value="jpg" />
f0b0037669e9 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" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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226 </conditional>
f0b0037669e9 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
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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228 </test>
1
f0b0037669e9 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
a9f156e31071 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit 2320dd4efe4d9c800588be55d10008212229703d
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230 <param name="alignment" value="input.fasta" />
1
f0b0037669e9 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">
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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232 <repeat name="include_positions">
f0b0037669e9 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" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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234 </repeat>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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235 <repeat name="include_positions">
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236 <param name="pos" value="10001-30000" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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237 </repeat>
f0b0037669e9 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">
f0b0037669e9 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" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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240 </repeat>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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241 <param name="exclude_ambig_pos" value="true" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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242 </section>
f0b0037669e9 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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244 <conditional name="sort">
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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245 <param name="order" value="--sort-by-mutations" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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246 <repeat name="positions">
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247 <param name="pos" value="3" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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248 </repeat>
f0b0037669e9 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">
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iuc
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250 <param name="pos" value="1" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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251 </repeat>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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parents: 0
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252 <repeat name="positions">
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253 <param name="pos" value="2" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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254 </repeat>
f0b0037669e9 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" />
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256 </conditional>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
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257 </section>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
parents: 0
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258 <conditional name="plot">
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iuc
parents: 0
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259 <param name="format" value="svg" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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260 <param name="transparent_background" value="true" />
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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261 </conditional>
f0b0037669e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit commit ec96004a9f92c601a3e6474efbe1bd408bed088d
iuc
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262 <assert_command>
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iuc
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263 <has_text text="--include-positions '1-10000' '10001-30000'" />
f0b0037669e9 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'" />
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265 <has_text text="--exclude-ambig-pos" />
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266 <has_text text="--sort-by-mutations 3,1,2" />
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267 <has_text text="--high-to-low" />
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268 </assert_command>
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269 <output name="snp_plot" ftype="svg">
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270 <assert_contents>
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271 <!-- check that the plot does NOT refer to excluded
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272 position 1059, uses darkseagreen (to highlight Ts) and
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273 transparent (i.e. NOT white) background -->
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274 <not_has_text text="&lt;!-- 1059 --&gt;" />
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275 <has_text text="style=&quot;fill: #8fbc8f" />
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276 <not_has_text text="style=&quot;fill: #ffffff&quot;" />
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277 </assert_contents>
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278 </output>
0
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279 </test>
1
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280 <test expect_num_outputs="1">
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281 <param name="alignment" value="input.fasta" />
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282 <section name="style">
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283 <conditional name="colouring">
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284 <param name="palette" value="" />
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285 <param name="parent1" value="USA_1" />
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286 <param name="parent2" value="USA_5" />
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287 </conditional>
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288 </section>
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289 <conditional name="plot">
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290 <param name="format" value="svg" />
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291 </conditional>
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292 <output name="snp_plot" ftype="svg">
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293 <assert_contents>
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294 <!-- check that the plot does mention position 1059,
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295 uses goldenrod and #EA5463 as colors (to
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296 indicate private and parent2 mutations, respectively, in
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297 recombi-mode) and uses a solid white background -->
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298 <has_text text="&lt;!-- 1059 --&gt;" />
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299 <has_text text="style=&quot;fill: #daa520" />
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300 <has_text text="style=&quot;fill: #ea5463" />
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301 <has_text text="style=&quot;fill: #ffffff&quot;" />
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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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306 <param name="alignment" value="input.fasta" />
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307 <section name="style">
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308 <conditional name="labels">
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309 <param name="choose" value="custom_csv" />
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310 <param name="source" value="custom_labels.csv" />
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311 <param name="names_column" value="ori" />
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312 <param name="labels_column" value="new" />
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313 </conditional>
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314 </section>
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315 <conditional name="plot">
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316 <param name="format" value="svg" />
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317 </conditional>
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318 <output name="snp_plot" ftype="svg">
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319 <assert_contents>
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320 <!-- check that the plot does not mention the original
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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>