Mercurial > repos > devteam > lastz

annotate lastz.xml @ 4:0acd9701676b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
author iuc
date Fri, 18 May 2018 16:58:24 -0400
parents c3767eaae954
children ec4affe27298
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4
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
iuc
parents: 3
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1 <tool id="lastz_wrapper_2" name="LASTZ" version="1.3.2">
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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2 <description>: align long sequences</description>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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3 <macros>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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4 <import>lastz_macros.xml</import>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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5 </macros>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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6 <requirements>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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7 <requirement type="package" version="@LASTZ_CONDA_VERSION@">lastz</requirement>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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8 <requirement type="package" version="1.7">samtools</requirement>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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9 <requirement type="package" version="3.4.2">r-base</requirement>
3
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
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10 <requirement type="package" version="1.0.6">bzip2</requirement>
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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11 </requirements>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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12 <command detect_errors="exit_code"><![CDATA[
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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13 lastz
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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14 @TARGET_INPUT_COMMAND_LINE@
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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15 ## If --self is set: perform self alignment and ignore the query
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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16 #if $where_to_look.self:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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17 '${where_to_look.self}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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18 #if $where_to_look.nomirror
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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19 '${where_to_look.nomirror}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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20 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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21 #else:
3
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
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22 @query_input@
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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23 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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24
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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25 ## WHERE TO LOOK --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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26
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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27 '${where_to_look.strand}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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28 #if str( $where_to_look.qhsplimit.qhsplimit_selector ) == "yes":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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29 #if $where_to_look.qhsplimit.qhsplimit_n:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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30 #if $where_to_look.qhsplimit.qhsplimit_nowarn:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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31 #if $where_to_look.qhsplimit.qhsplimit_keep:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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32 '--queryhsplimit=${where_to_look.qhsplimit.qhsplimit_keep},${where_to_look.qhsplimit.qhsplimit_nowarn}:${where_to_look.qhsplimit.qhsplimit_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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33 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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34 '--queryhsplimit=${where_to_look.qhsplimit.qhsplimit_nowarn}:${where_to_look.qhsplimit.qhsplimit_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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35 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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36 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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37 '--queryhsplimit=${where_to_look.qhsplimit.qhsplimit_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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38 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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39 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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40 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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41
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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42 #if $where_to_look.qhspbest:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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43 '--queryhspbest=${where_to_look.qhspbest}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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44 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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45
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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46 #if str( $where_to_look.qdepth.qdepth_selector ) == "yes":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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47 #if $where_to_look.qdepth.qdepth_n:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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48 #if $where_to_look.qdepth.qdepth_nowarn and not $where_to_look.qdepth.qdepth_keep:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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49 '--querydepth=${where_to_look.qdepth.qdepth_nowarn}:${where_to_look.qdepth.qdepth_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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50 #elif not $where_to_look.qdepth.qdepth_nowarn and $where_to_look.qdepth.qdepth_keep:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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51 '--querydepth=${where_to_look.qdepth.qdepth_keep}:${where_to_look.qdepth.qdepth_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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52 #elif $where_to_look.qdepth.qdepth_nowarn and $where_to_look.qdepth.qdepth_keep:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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53 '--querydepth=${where_to_look.qdepth.qdepth_keep},${where_to_look.qdepth.qdepth_nowarn}:${where_to_look.qdepth.qdepth_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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54 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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55 '--querydepth=${where_to_look.qdepth.qdepth_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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56 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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57 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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58 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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59
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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60 ## SCORING --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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61
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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62 #if $scoring.score_file:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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63 '--scores=${scoring.score_file}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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64 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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65
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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66 #if str( $scoring.match.match_selector ) == "yes":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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67 #if $scoring.match.match_reward:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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68 #if $scoring.match.match_penalty:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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69 '--match=${scoring.match.match_reward},${scoring.match.match_penalty}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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70 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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71 '--match=${scoring.match.match_reward}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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72 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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73 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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74 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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75 #if str( $scoring.gap.gap_selector ) == "yes":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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76 #if $scoring.gap.gap_extend:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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77 #if $scoring.gap.gap_open:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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78 '--gap=${scoring.gap.gap_open},${scoring.gap.gap_extend}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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79 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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80 '--gap=${scoring.gap.gap_extend}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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81 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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82 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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83 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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84 #if $scoring.ambigN:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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85 '${scoring.ambigN}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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86 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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87 #if $scoring.ambigIUPAC:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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88 '${scoring.ambigIUPAC}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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diff changeset
89 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
90
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
91 ## SEEDING --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
92
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
93 #if str( $seeding.seed.seed_selector ) == "pre_set":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
94 '${seeding.seed.pre_set_seeds}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
95 #elif str( $seeding.seed.seed_selector ) == "len":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
96 '--seed=match${seeding.seed.seed_match}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
97 #elif str( $seeding.seed.seed_selector ) == "half_len":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
98 '--seed=half${seeding.seed.seed_half}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
99 #elif str( $seeding.seed.seed_selector ) == "pattern":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
100 '--seed=${seeding.seed.pattern}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
101 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
102 #if str( $seeding.transitions ) != "--transition":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
103 '${seeding.transitions}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
104 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
105 #if str( $seeding.seed_filer.seed_filer_selector ) == "yes":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
106 #if $seeding.seed_filer.filter_match:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
107 #if $seeding.seed_filer.filter_tr:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
108 '--filter=${seeding.seed_filer.filter_tr},${seeding.seed_filer.filter_match}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
109 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
110 '--filter=${seeding.seed_filer.filter_match}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
111 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
112 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
113 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
114
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iuc
parents:
diff changeset
115 ## FINDING HSPs --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
116
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iuc
parents:
diff changeset
117 #if $hsp.gfextend:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
118 '${hsp.gfextend}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
119 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
120 #if $hsp.nogfextend
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
121 '${hsp.nogfextend}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
122 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
123 #if str( $hsp.hsp_method.hsp_method_selector ) == "match":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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diff changeset
124
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iuc
parents:
diff changeset
125 #if $hsp.hsp_method.exact:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
126 '--exact=${hsp.hsp_method.exact}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
127 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
128 #elif str( $hsp.hsp_method.hsp_method_selector ) == "mismatch":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
129
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iuc
parents:
diff changeset
130 #if $hsp.hsp_method.mismatch_count and $hsp.hsp_method.mismatch_length:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
131 '--mismatch=${hsp.hsp_method.mismatch_count},${hsp.hsp_method.mismatch_length}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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diff changeset
132 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
133 #elif str( $hsp.hsp_method.hsp_method_selector ) == "x":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
134
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iuc
parents:
diff changeset
135 #if $hsp.hsp_method.xdrop:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
136 '--xdrop=${hsp.hsp_method.xdrop}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
137 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
138
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iuc
parents:
diff changeset
139 #if $hsp.hsp_method.hspthresh:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
140 '--hspthresh=${hsp.hsp_method.hspthresh}'
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iuc
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diff changeset
141 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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diff changeset
142
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iuc
parents:
diff changeset
143 #if $hsp.hsp_method.hspthresh_top:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
144 '--hspthresh=top${hsp.hsp_method.hspthresh_top}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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diff changeset
145 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
146
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iuc
parents:
diff changeset
147 #if $hsp.hsp_method.hspthresh_top_percent:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
148 '--hspthresh=top${hsp.hsp_method.hspthresh_top_percent}%'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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diff changeset
149 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
150 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
151 #if $hsp.entropy:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
152 '${hsp.entropy}'
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iuc
parents:
diff changeset
153 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
154 #if $hsp.entropy_report:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
155 '${hsp.entropy_report}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
156 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
157 #if $hsp.noentropy:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
158 '${hsp.noentropy}'
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iuc
parents:
diff changeset
159 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
160
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
161 ## CHAINING --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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parents:
diff changeset
162
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
163 #if $chaining.chain:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
164 '${chaining.chain}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
165 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
166 #if str( $chaining.chaning_penalties.chaning_penalties_selector ) == "yes":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
167 #if $chaining.chaning_penalties.diag and $chaining.chaning_penalties.anti:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
168 '--chain=${chaining.chaning_penalties.diag},${chaining.chaning_penalties.anti}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
169 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
170 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
171
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iuc
parents:
diff changeset
172 ## GAPPED EXTENSION --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
173
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iuc
parents:
diff changeset
174 #if $gap_ext.gapped:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
175 '${gap_ext.gapped}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
176 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
177 #if $gap_ext.nogapped:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
178 '${gap_ext.nogapped}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
179 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
180 #if $gap_ext.ydrop:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
181 '--ydrop=${gap_ext.ydrop}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
182 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
183 #if $gap_ext.noytrim:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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diff changeset
184 '${gap_ext.noytrim}'
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185 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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diff changeset
186 #if $gap_ext.gappedthresh:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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187 '--gappedthresh=${gap_ext.gappedthresh}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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parents:
diff changeset
188 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
189 #if $gap_ext.allgappedbounds:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
190 '${gap_ext.allgappedbounds}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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diff changeset
191 #end if
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192
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193 ## FILTERING --------------------------------
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194
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195 #if $filters.identity.id_min:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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diff changeset
196 #if $filters.identity.id_max:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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197 '--filter=identity:${filters.identity.id_min}..${filters.identity.id_max}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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198 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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199 '--filter=identity:${filters.identity.id_min}'
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200 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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201 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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diff changeset
202 #if $filters.continuity.cont_min:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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diff changeset
203 #if $filters.continuity.cont_max:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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204 '--filter=continuity:${filters.continuity.cont_min}..${filters.continuity.cont_max}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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205 #else:
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iuc
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diff changeset
206 '--filter=continuity:${filters.continuity.cont_min}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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207 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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208 #end if
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iuc
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209 #if $filters.coverage.cov_min:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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210 #if $filters.coverage.cov_max:
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iuc
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211 '--filter=coverage:${filters.coverage.cov_min}..${filters.coverage.cov_max}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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212 #else:
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iuc
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213 '--filter=coverage:${filters.coverage.cov_min}'
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diff changeset
214 #end if
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215 #end if
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216 #if $filters.filter_nmatch:
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iuc
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217 '--filter=nmatch:${filters.filter_nmatch}'
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diff changeset
218 #end if
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iuc
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219 #if $filters.filter_nmatch_percent:
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iuc
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220 '--filter=nmatch:${filters.filter_nmatch_percent}%'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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diff changeset
221 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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222 #if $filters.filter_nmismatch:
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223 '--filter=nmismatch:0..${filters.filter_nmismatch}'
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diff changeset
224 #end if
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iuc
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225 #if $filters.filter_ngap:
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iuc
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226 '--filter=ngap:0..${filters.filter_ngap}'
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iuc
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227 #end if
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iuc
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228 #if $filters.filter_cgap:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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229 '--filter=cgap:0..${filters.filter_cgap}'
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230 #end if
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231 #if $filters.notrivial:
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iuc
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232 '${filters.notrivial}'
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diff changeset
233 #end if
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234
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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235 ## INTERPOLATION --------------------------------
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236
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237 #if $interpolation.inner:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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238 '--inner=${interpolation.inner}'
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239 #end if
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240
4
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diff changeset
241 ## HOUSEKEEPING ----------------------------------
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parents: 3
diff changeset
242
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
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diff changeset
243 --traceback=160M
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parents: 3
diff changeset
244
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
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diff changeset
245
2
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246 ## OUTPUT FORMATS --------------------------------
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247
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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248 #if str( $output_format.out.format ) == "bam":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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249 '--format=${output_format.out.bam_options}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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250 #elif str( $output_format.out.format ) == "general_def":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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diff changeset
251 --format=general-
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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252 #elif str( $output_format.out.format ) == "maf":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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diff changeset
253 '--format=${output_format.out.maf_type}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
254 #elif str( $output_format.out.format ) == "blastn":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
255 --format=BLASTN-
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iuc
parents:
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256 #elif str( $output_format.out.format ) == "general_full":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
257 '--format=general-:${output_format.out.fields}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
258 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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diff changeset
259 --action:target=multiple
4
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
iuc
parents: 3
diff changeset
260 $output_format.rplot
2
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iuc
parents:
diff changeset
261 #if str( $output_format.out.format ) == "bam":
4
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
iuc
parents: 3
diff changeset
262 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '${output}'
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
263 #else:
4
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
iuc
parents: 3
diff changeset
264 > '${output}'
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
265 #end if
4
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
iuc
parents: 3
diff changeset
266 #if $output_format.rplot:
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
iuc
parents: 3
diff changeset
267 &&
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
iuc
parents: 3
diff changeset
268 Rscript $r_plot > /dev/null 2>&1
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iuc
parents: 3
diff changeset
269 #end if
2
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270
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iuc
parents:
diff changeset
271 ]]>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
272 </command>
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iuc
parents:
diff changeset
273 <configfiles>
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iuc
parents:
diff changeset
274 <configfile name="r_plot">
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iuc
parents:
diff changeset
275 <![CDATA[
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
276 #!/usr/bin/env Rscript
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277 ## Setup R error handling to go to stderr
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278 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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279 ## Only produce image when 'plot.r' actually contains data
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280 if(file.info('plot.r')\$size>0){
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281 x <- read.table("plot.r", as.is=TRUE)
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282 png("${out_plot}", width=640, height=640, res=72)
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283 plot(x, type='l', xlab="target", ylab="query", main="plot")
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284 dev.off()
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285 }
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286 ]]>
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287 </configfile>
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288 </configfiles>
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289 <inputs>
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290 <expand macro="target_input"/>
3
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291 <param name="query" format="fasta,fastq,fasta.gz,fastq.gz,fastq.bz2" type="data" label="Select QUERY sequence(s)" help="These are the sequences that you are aligning against TARGET"/>
2
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292
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293 <section name="where_to_look" expanded="False" title="Where to look">
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294 <param name="strand" type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus">
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295 <option value="--strand=both" selected="True">Both</option>
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296 <option value="--strand=plus">Plus</option>
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297 <option value="--strand=minus">Minus</option>
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298 </param>
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299 <param name="self" type="boolean" display="radio" truevalue="--self" falsevalue="" checked="False" argument="--self" label="Perform a self-alignment: the target sequence is also the query." help="Computation is more efficient than it would be without this option, since only one of each mirror-image pair of alignment blocks is processed (the other, redundant one is skipped during processing, but re-created in the output). Also, the trivial self-alignment block along the main diagonal is omitted from the output. THIS OPTION CANNOT BE USED IF THE TARGET IS COMPRIZED OF MULTIPLE SEQUENCES"/>
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300 <param name="nomirror" type="boolean" display="radio" truevalue="--nomirror" falsevalue="" checked="False" label="Inhibit the re-creation of mirror-image alignments." argument="--nomirror" help="Output consists of only one copy of each meaningful alignment block in a self-alignment. This option is only applicable when the ‑‑self option is used."/>
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301 <conditional name="qhsplimit">
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302 <param name="qhsplimit_selector" type="select" display="radio" label="Set HSP limit" argument="--queryhsplimit">
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303 <option value="yes">Yes</option>
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304 <option value="no" selected="true">No</option>
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305 </param>
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306 <when value="yes">
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307 <param name="qhsplimit_n" optional="true" type="integer" label="Discard queries that have more than N HSPs" help="Any queries that exceed this limit are reported as a warning (to stderr), and no alignments are reported. This is useful for mapping reads to a reference genome, when some reads align to too many places in the reference."/>
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308 <param name="qhsplimit_nowarn" type="boolean" truevalue="nowarn" display="radio" checked="False" label=" Withhold warnings for queries that exceed the limit set above"/>
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309 <param name="qhsplimit_keep" type="boolean" truevalue="keep" display="radio" checked="False" label="Keep queries that exceed the limit and supress warnings" help="For such a query, the first N HSPs found are passed along to downstream processing. Note that the HSPs reported are not the best N HSPs. They are simply the first N found; they very likely have a positional bias."/>
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310 </when>
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311 <when value="no">
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312 <!-- Do nothing -->
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313 </when>
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314 </conditional>
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315 <param name="qhspbest" type="integer" optional="true" label="For queries that have more than N HSPs, discard any HSPs that score below the Nth best." help="This is useful for mapping reads to a reference genome, when some reads align to too many places in the reference."/>
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316 <conditional name="qdepth">
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317 <param name="qdepth_selector" type="select" display="radio" label="Set ratio of aligned bases to query length" argument="--querydepth">
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318 <option value="yes">Yes</option>
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319 <option value="no" selected="true">No</option>
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320 </param>
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321 <when value="yes">
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322 <param name="qdepth_n" optional="true" type="integer" label="Stop processing gapped alignments for a query/strand if its ratio of aligned bases to query length exceeds" help="This is a real number that corresponds to a depth of coverage threshold. For example, a value of 5.0 would cause termination once a query/strand has an average of five alignments for every base in the query. The numerator is the number of matches or substitutions (but not gaps); the denominator is the length of the query sequence. The purpose of this option is one of saving time. It is useful for automatically terminating the processing of queries with high repeat content, for which other methods of dealing with repetitive content fail. Moreover, back-end filtering options are not considered. In other words, matches are counted for any alignment that meets the scoring threshold, regardless of whether that alignment would be reported. The justification is that we are trying to abort the processing of queries that have too many bounding alignments in the DP matrix, and back-end filtering occurs later in the process."/>
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323 <param name="qdepth_keep" type="boolean" truevalue="keep" display="radio" checked="False" label="Warnings for queries that exceed the limit are witheld" help="Note that the alignments reported are not guaranteed to be the highest scoring alignments that would achieve the threshold. They are simply the first alignments found. In other words, the purpose of this option is one of saving time, not one of finding optimal alignments."/>
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324 <param name="qdepth_nowarn" type="boolean" truevalue="nowarn" display="radio" checked="False" label="Same as above but any alignments discovered for this query/strand, before it exceeds the threshold, are reported."/>
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325 </when>
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326 <when value="no">
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327 <!-- Do nothing -->
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328 </when>
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329 </conditional>
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330 </section>
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331 <section name="scoring" expanded="false" title="Scoring">
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332 <param name="score_file" type="data" format="txt" optional="true" argument="--scores" label="Read the substitution scores and gap penalties (and possibly other options) from a scoring file (see help below for file fomat description)." help="This option cannot be used in conjunction with ‑‑match or inference."/> <!--TODO EDIT INFERENCE -->
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333 <conditional name="match">
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334 <param name="match_selector" type="select" display="radio" label="Set the score values for a match and mismatch" argument="--match" help="Note that specifying ‑‑match changes the defaults for some of the other options (e.g. the scoring penalties for gaps, and various extension thresholds), as described in respective sections of LASTZ manual. The regular defaults are chosen for compatibility with BLASTZ, but since BLASTZ doesn't support ‑‑match, LASTZ infers that you are not expecting BLASTZ compatibility for this run, so it is free to use improved defaults. THIS OPTION CANNOT BE USED WITH --scores">
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335 <option value="yes">Yes</option>
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336 <option value="no" selected="true">No</option>
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337 </param>
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338 <when value="yes">
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339 <param name="match_reward" type="integer" optional="true" label="Score value for a match"/>
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340 <param name="match_penalty" type="integer" optional="true" label="Score value for a mismatch"/>
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341 </when>
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342 <when value="no">
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343 <!-- Do nothing -->
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344 </when>
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345 </conditional>
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346 <conditional name="gap">
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347 <param name="gap_selector" type="select" display="radio" label="Set the score penalties for opening and extending a gap" argument="--gap" help="These are specified as positive values; subtraction is implicitly assumed. Note that the first base in a gap incurs the sum of both penalties. This option is only valid if gapped extension is being performed, and cannot be used in conjunction with inference. These values specified on the command line override any corresponding values from a file provided with ‑‑scores.">
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348 <option value="yes">Yes</option>
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349 <option value="no" selected="true">No</option>
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350 </param>
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351 <when value="yes">
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352 <param name="gap_open" type="integer" optional="true" label="Gap opening penalty"/>
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353 <param name="gap_extend" type="integer" optional="true" label="Gap extension penalty"/>
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354 </when>
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355 <when value="no">
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356 <!-- Do nothing -->
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357 </when>
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358 </conditional>
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359 <param name="ambigN" type="boolean" truevalue="--ambiguous=n" checked="false" label="Treat each N in the input sequences as an ambiguous nucleotide" argument="--ambiguous=n" help="Substitutions with N are scored as zero, instead of using the fill_score value from the scoring file (which is -100 by default)."/>
4
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360 <param name="ambigIUPAC" type="boolean" truevalue="--ambiguous=iupac" checked="true" label="Treat each of the IUPAC-IUB ambiguity codes (B, D, H, K, M, R, S, V, W, and Y, as well as N) in the input sequences as a completely ambiguous nucleotide." argument="--ambiguous=iupac" help="Substitutions with these characters are scored as zero, instead of using the fill_score value from the scoring file (which is -100 by default)."/>
2
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361 </section>
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362 <section name="seeding" expanded="false" title="Seeding">
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363 <conditional name="seed">
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364 <param name="seed_selector" type="select" display="radio" label="Select seed type">
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365 <option value="defaults" selected="true">Use defaults</option>
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366 <option value="pre_set">Use pre-set values</option>
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367 <option value="len">Set length</option>
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368 <option value="half_len">Set half length</option>
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369 <option value="pattern">Set pattern</option>
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370 </param>
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371 <when value="defaults">
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372 <!-- Do nothing -->
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373 </when>
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374 <when value="pre_set">
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375 <param name="pre_set_seeds" type="select" display="radio" label="Select seed pattern" help="Select between 12of19 seed (19-bp word with matches in 12 specific positions: 1110100110010101111) or 14of22 seed (22-bp word with matches in 14 specific positions: 1110101100110010101111). 0 = mismatch, 1 = match" argument="--seed=12of19,--seed=14of22">
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376 <option value="--seed=12of19">12of19</option>
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377 <option value="--seed=14of22">14of22</option>
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378 </param>
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379 </when>
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diff changeset
380 <when value="len">
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381 <param name="seed_match" type="integer" optional="true" label="Set seed length" help="Seeds require a N-bp word with matches in all positions" argument="--seed=match" />
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382 </when>
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383 <when value="half_len">
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384 <param name="seed_half" type="integer" optional="true" label="Set seed length" help="Seeds requires N-bp word with matches or transitions in all positions" argument="--seed=half" />
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diff changeset
385 </when>
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diff changeset
386 <when value="pattern">
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387 <param name="pattern" type="text" size="25" optional="true" argument="--seed=PATTERN" label="Specify an arbitrary pattern" help="Use 1s, 0s, and Ts for seed discovery (e.g., 1110100110010101111 where 1 = match, 0 = mismatch, T = transition)" />
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diff changeset
388 </when>
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389 </conditional>
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390 <param name="transitions" type="select" display="radio" label="Allow transitions" help="In each seed, specify how many match positions can be transition(s) instead">
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391 <option value="--transition" selected="true">One</option>
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392 <option value="--transition=2">Two</option>
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393 <option value="--notransition">None</option>
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diff changeset
394 </param>
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395 <conditional name="seed_filer">
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396 <param name="seed_filer_selector" type="select" display="radio" label="Filter seeds" argument="--filter">
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397 <option value="yes">Yes</option>
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398 <option value="no" selected="true">No</option>
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diff changeset
399 </param>
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diff changeset
400 <when value="yes">
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401 <param name="filter_tr" type="integer" optional="true" label="Number of transitions" help="Allowing no more than this number of transversions. If not specified, any number of transversions is allowed (they are not limited)" />
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402 <param name="filter_match" type="integer" optional="true" label="Number of matches" help="Require at least this many exact matches"/>
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diff changeset
403 </when>
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404 <when value="no">
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405 <!-- Do nothing -->
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diff changeset
406 </when>
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407 </conditional>
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408 </section>
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409 <section name="hsp" expanded="false" title="HSPs (Gap-free extension)">
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410 <param name="gfextend" type="boolean" truevalue="--gfextend" checked="false" argument="--gfextend" label="Perform gap-free extension of seeds to HSPs" help="This will take into account other papermeters in this section"/>
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411 <param name="nogfextend" type="boolean" truevalue="--nogfextend" argument="--nogfextend" label="Skip the gap-free extension stage" help="Instead, pass the seeds along to the next specified stage.It is not recommended to use --nogfextend without also using --nogapped."/>
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412 <conditional name="hsp_method">
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413 <param name="hsp_method_selector" type="select" display="radio" label="Select HSP finding method">
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414 <option value="none" selected="true">None</option>
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415 <option value="match">Match extension</option>
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416 <option value="mismatch">Mismatch extension</option>
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417 <option value="x">X-drop extension</option>
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418 </param>
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diff changeset
419 <when value="none">
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420 <!-- Do nothing -->
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421 </when>
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422 <when value="match">
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423 <param name="exact" type="integer" optional="true" argument="--exact" label="Find HSPs using the exact match extension method with the given length threshold" help="This is instead of using the x-drop method"/>
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424 </when>
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425 <when value="mismatch">
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426 <param name="mismatch_count" type="integer" optional="true" label="Specify number of mismatches"/>
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427 <param name="mismatch_length" type="integer" min="1" max="50" optional="true" label="Specify length threshold" help="Find HSPs using the mismatch extension method with the given length threshold and allowing specified number of mismatches" argument="--mismatch"/>
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428 </when>
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429 <when value="x">
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430 <param name="xdrop" type="integer" optional="true" argument="--xdrop" label="Find HSPs using the x-drop extension method with this threshold" help="The dropoff setting determines the endpoints of each gap-free segment: the extension of each seed is stopped when its cumulative score drops off by more than the given threshold from the maximum seen so far."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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431 <param name="hspthresh" type="integer" optional="true" argument="--hspthresh" label="Set the score threshold for the x-drop extension method" help="HSPs scoring lower are discarded"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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432 <param name="hspthresh_top" type="integer" optional="true" argument="--hspthresh=top" label="Set an adaptive score threshold for the x-drop extension method" help="HSPs scoring lower are discarded. The score threshold is chosen to limit the number of target sequence bases in HSPs to about this value (or possibly a little higher in case of ties, etc.)."/>
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433 <param name="hspthresh_top_percent" type="integer" optional="true" argument="--hspthresh=top%" label="Set an adaptive score threshold for the x-drop extension method" help="HSPs scoring lower are discarded. The score threshold is chosen to limit the number of target sequence bases in HSPs to about this perentage value (or possibly a little higher in case of ties, etc.)."/>
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434 </when>
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435 </conditional>
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436 <param name="entropy" type="boolean" truevalue="--entropy" checked="false" label="Adjust for entropy when qualifying HSPs in the x-drop extension method" help="Those that score just slightly above the HSP threshold are adjusted downward according to the entropy of their nucleotides, and any that then fall below the threshold are discarded."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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437 <param name="entropy_report" type="boolean" truevalue="--entropy=report" checked="false" label="Adjust for entropy when qualifying HSPs in the x-drop extension method, and report (to stderr) any HSPs that are discarded as a result." help="Reported HSPs are printed to stderr"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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438 <param name="noentropy" type="boolean" truevalue="--noentropy" checked="false" label="Don't adjust for entropy when qualifying HSPs"/>
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439 </section>
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440 <section name="chaining" expanded="false" title="Chaining">
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441 <param name="chain" type="boolean" truevalue="--chain" checked="false" argument="--chain" label="Perform chaining of HSPs with no penalties"/>
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442 <conditional name="chaning_penalties">
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443 <param name="chaning_penalties_selector" type="select" display="radio" argument="--chain=" label="Perform chaining with penalties">
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444 <option value="yes">Yes</option>
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445 <option value="no" selected="true">No</option>
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446 </param>
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447 <when value="yes">
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448 <param name="diag" type="integer" optional="true" label="Penalty for diagonal in dynamic programming matrix"/>
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449 <param name="anti" type="integer" optional="true" label="Penalty for anti-diagonal in dynamic programming matrix" help="These are specified as positive values; subtraction from the score is implicitly assumed."/>
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450 </when>
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451 <when value="no">
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452 <!-- Do nothing -->
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453 </when>
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454 </conditional>
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455 </section>
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456 <section name="gap_ext" expanded="false" title="Gapped extension">
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457 <param name="gapped" type="boolean" truevalue="--gapped" argument="--gapped" label="Perform gapped extension of HSPs" help="Extension of HSPs (or seeds, if gap-free extension is not performed), is performed after first reducing them to anchor points."/>
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458 <param name="nogapped" type="boolean" truevalue="--nogapped" argument="--nogapped" label="Skip the gapped extension stage" help="This means that interpolation must also be skipped, since it is not allowed without gapped extension"/>
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459 <param name="ydrop" type="integer" optional="true" argument="--ydrop" label="Set the threshold for terminating gapped extension" help="This restricts the endpoints of each local alignment by limiting the local region around each anchor in which extension is performed. The boundary of this region in the dynamic programming matrix is formed by the points where the cumulative score has dropped off by more than the given threshold from the maximum seen so far."/>
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460 <param name="noytrim" type="boolean" truevalue="--noytrim" argument="--noytrim" label="If y-drop extension encounters the end of the sequence, extend the alignment to the end of the sequence rather than trimming it back to the location giving the maximum score" help="This is highly recommended when either the target or query sequences are short reads (say, less than 100 bases), to prevent y-drop mismatch shadow."/>
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461 <param name="gappedthresh" type="integer" optional="true" argument="--gappedthresh" label="Set the threshold for gapped extension" help="Alignments scoring lower than that value are discarded. When used along with the x-drop method for gap-free extension, this value is generally set at least as high as the HSP threshold. Setting it lower has no effect, since at worst the HSP itself would always qualify (both extension stages use the same scoring matrix)."/>
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462 <param name="allgappedbounds" type="boolean" truevalue="--allgappedbounds" argument="--allgappedbounds" label="Revert to handling bounding alignments the way they were handled in BLASTZ."/>
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463 </section>
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464 <section name="filters" expanded="false" title="Filtering">
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465 <section name="identity" expanded="true" title="Filter alignments by percent identity">
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466 <param name="id_min" type="integer" min="0" max="100" optional="true" label="Minimum identity"/>
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467 <param name="id_max" type="integer" min="0" max="100" optional="true" argument="--filter=identity" label="Maximum identity (optional)" help="0 ≤ min ≤ max ≤ 100 percent. Identity is the percentage of aligned bases that are matches. Alignment blocks outside the given range are discarded."/>
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468 </section>
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469 <section name="continuity" expanded="false" title="Filter alignments by continuity">
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470 <param name="cont_min" type="integer" min="0" max="100" optional="true" label="Minimum continuity"/>
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471 <param name="cont_max" type="integer" min="0" max="100" optional="true" argument="--filter=continuity" label="Maximum continuity (optional)" help="0 ≤ min ≤ max ≤ 100 percent. Continuity is the percentage of alignment columns that are not gaps. Alignment blocks outside the given range are discarded."/>
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472 </section>
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473 <section name="coverage" expanded="false" title="Filter alignments by coverage">
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474 <param name="cov_min" type="integer" min="0" max="100" optional="true" label="Minimum coverage"/>
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475 <param name="cov_max" type="integer" min="0" max="100" optional="true" argument="--filter=coverage" label="Maximum coverage (optional)" help=" 0 ≤ min ≤ max ≤ 100 percent. Coverage is the percentage of the entire target or query sequence (whichever is shorter) that is included in the alignment block. Blocks outside the given range are discarded."/>
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476 </section>
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477 <param name="filter_nmatch" type="integer" min="1" optional="true" argument="--filter=nmatch" label="Filter alignments by how many bases match" help="Requiring at least this number of matched bases, min > 0. Match count is the number of matched bases in the alignment."/>
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478 <param name="filter_nmatch_percent" type="integer" min="1" optional="true" argument="--filter=nmatch%" label="Filter alignments by how many bases match expressed as percentage" help="e.g., percentage of the query length."/>
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479 <param name="filter_nmismatch" type="integer" min="0" optional="true" argument="--filter=nmismatch:0.." label="Filter alignments by the number of mismatches" help="Allow no more than this number of mismatched bases. Mismatch count, or nmismatch, is the number of aligned bases in the alignment that are mismatches (substitutions)."/>
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480 <param name="filter_ngap" type="integer" min="0" optional="true" argument="--filter=ngap:0.." label="Filter alignments by the number of gaps" help="Allow no more than this number of gaps. Gap count, or ngap, is the number of runs of gapped columns in the alignment (each run is counted as one gap)."/>
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481 <param name="filter_cgap" type="integer" min="0" optional="true" argument="--filter=cgap:0.." label="Filter alignments by the number of gap columns" help="Allow no more than this number of gaps. Gap column count, or cgap, is the number of gapped columns in the alignment (each column is counted as one gap)."/>
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482 <param name="notrivial" type="boolean" truevalue="--notrivial" argument="--notrivial" label="Do not output a trivial self-alignment block if the target and query sequences are identical" help="Note that using ‑‑self automatically enables this option."/>
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483 </section>
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484 <section name="interpolation" expanded="false" title="Interpolation">
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485 <param name="inner" type="integer" optional="true" argument="--inner" label="Perform additional alignment between the gapped alignment blocks, using (presumably) more sensitive alignment parameters" help="This value is used as the threshold for both the gap-free and gapped extension sub-stages; see the discussion of interpolation for more details. This option is only valid if gapped extension is performed."/>
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486 </section>
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487 <section name="output_format" expanded="false" title="Output">
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488 <conditional name="out">
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489 <param name="format" type="select" display="radio" label="Specify the output format">
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490 <option value="bam" selected="true">BAM --format=sam)</option>
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491 <option value="general_def">General default (--format=general)</option>
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492 <option value="general_full">Customized general (‑‑format=general[:fields])</option>
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493 <option value="maf">MAF (--format=maf)</option>
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494 <option value="blastn">blastn (--format=BLASTN)</option>
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495 </param>
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496 <when value="bam">
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497 <param name="bam_options" type="select" display="radio" argument="--format=sam, --format=softsam" label="Select a BAM flavor to output" help="Lastz actually outputs SAM data but Galaxy converts it into BAM to save space. For alignments that don't reach the end of a query, ‑‑format=sam uses 'hard clipping', while ‑‑format=softsam uses 'soft clipping'. See the section on 'clipped alignment' in the SAM specification for an explanation of what this means. The options ‑‑format=sam- and ‑‑format=softsam- suppress the SAM header lines. This makes them suitable for concatenating output from multiple runs. If you need to specify readgroup information: use AddOrEplaceReadGroups from Picard package">
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498 <option value="sam" selected="true">BAM</option>
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499 <option value="softsam">soft-clipped BAM</option>
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500 <option value="sam-">BAM without header</option>
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501 <option value="softsam-">soft-clipped BAM without header</option>
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502 </param>
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503 </when>
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504 <when value="general_def">
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505 <!-- Do nothing -->
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506 </when>
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507 <when value="general_full">
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508 <param name="fields" type="select" display="checkboxes" multiple="true" label="Select which fields to include" argument="--format=general-[:fields]">
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509 <option value="score" selected="true">score: Score of the alignment block</option>
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510 <option value="name1" selected="true">name1: Name of the target sequence</option>
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511 <option value="number1">number1: Number of the target sequence within the target file</option>
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512 <option value="strand1" selected="true">strand1: Target sequence strand </option>
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513 <option value="size1" selected="true">size1: Size of the entire target sequence</option>
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diff changeset
514 <option value="start1">start1: Starting position of the alignment block in the target, origin-one</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
515 <option value="zstart1" selected="true">zstart1: Starting position of the alignment block in the target, origin-zero</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
516 <option value="end1" selected="true">end1: Ending position of the alignment block in the target</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
517 <option value="length1">length1: Length of the alignment block in the target (excluding gaps)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
518 <option value="text1">text1: Aligned characters in the target, including gap characters</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
519 <option value="qalign1">qalign1: The target quality sequence (if there is one) correpsonding to aligned characters</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
520 <option value="nucs1">nucs1: The entire target sequence</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
521 <option value="name2" selected="true">name2: Name of the query sequence</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
522 <option value="number2">number2: Number of the query sequence within the query file</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
523 <option value="strand2" selected="true">strand2: Query sequence strand</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
524 <option value="size2" selected="true">size2: Size of the entire query sequence</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
525 <option value="start2">start2: Starting position of the alignment block in the query, origin-one</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
526 <option value="zstart2" selected="true">zstart2: Starting position of the alignment block in the query, origin-one</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
527 <option value="end2" selected="true">end2: Ending position of the alignment block in the query</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
528 <option value="length2">length2: Length of the alignment block in the query (excluding gaps)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
529 <option value="text2">text2: Aligned characters in the query, including gap characters</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
530 <option value="qalign2">qalign2: The query quality sequence (if there is one) correpsonding to aligned characters</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
531 <option value="nucs2">nucs2: The entire query sequence</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
532 <option value="nmatch">nmatch: Match count</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
533 <option value="nmismatch">nmismatch: Mismatch count</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
534 <option value="ncolumn">ncolumn: Number of columns in the block. This includes matches, mismatches (substitutions), and gaps</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
535 <option value="npair">npair: Number of aligned bases in the block that are matches or mismatches (substitutions)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
536 <option value="ngap">ngap: Gap count, the number of gaps in the block, counting each run of gapped columns as a single gap</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
537 <option value="cgap">cgap: Gap column count, the number of gaps in the block, counting each gapped column as a separate gap</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
538 <option value="diff">diff: Differences between what would be written for text1 and text2</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
539 <option value="cigar">cigar: A CIGAR-like representation of the alignment’s path</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
540 <option value="cigarx">cigarx: Same as cigar, but uses a newer syntax that distinguishes matches from substitutions</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
541 <option value="identity" selected="true">identity: Fraction of aligned bases in the block that are matches </option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
542 <option value="idfrac">idfrac: Fraction of aligned bases in the block that are matches </option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
543 <option value="id%" selected="true">id% Fraction of aligned bases in the block that are matches (as %)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
544 <option value="blastid%">blastid%: Fraction of the alignment block that is matches, as would be reported by NCBI BLAST</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
545 <option value="continuity">continuity: Rate of non-gaps (non-indels) in the alignment block</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
546 <option value="confrac">confrac: Rate of non-gaps (non-indels) in the alignment block (as fraction)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
547 <option value="con%">con%: Rate of non-gaps (non-indels) in the alignment block (as %)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
548 <option value="coverage" selected="true">coverage: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
549 <option value="covfrac">covfrac: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as fraction)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
550 <option value="cov%" selected="true">cov%: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as %)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
551 <option value="diagonal">diagonal: The diagonal of the start of the alignment block in the DP matrix, expressed as an identifying number start1-start2</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
552 <option value="shingle">shingle: A measurement of the shingle overlap between the target and the query</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
553 <option value="number">number: The alignment number, counted as alignments are written to output (1-base)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
554 <option value="znumber">znumber: The alignment number, counted as alignments are written to output (0-base)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
555 <sanitizer invalid_char="">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
556 <valid initial="string.letters,string.digits"><add value="%" /> </valid>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
557 </sanitizer>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
558 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
559 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
560 <when value="maf">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
561 <param name="maf_type" type="select" display="radio" argument="--format=maf" label="Seleat MAF flavor" help="MAF is a multiple alignment format developed at UCSC">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
562 <option value="maf">MAF</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
563 <option value="maf+">MAF with additional stats</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
564 <option value="maf-">MAF without header and comments</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
565 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
566 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
567 <when value="blastn">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
568 <!-- Do nothing -->
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
569 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
570 </conditional>
4
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
iuc
parents: 3
diff changeset
571 <param name="rplot" type="boolean" truevalue="--rdotplot=plot.r" falsevalue="" checked="false" argument="--rdotplot" label="Create a dotplot representation of alignments?" help="The dotplot is only useful if query and target contain exactly one sequence each"/>
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
572 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
573 </inputs>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
574 <outputs>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
575 <data format="tabular" name="output" label="${tool.name} on ${on_string}: mapped reads">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
576 <change_format>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
577 <when input="output_format.out.format" value="bam" format="bam" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
578 <when input="output_format.out.format" value="maf" format="maf" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
579 </change_format>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
580 </data>
4
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
iuc
parents: 3
diff changeset
581 <data format="png" name="out_plot" label="${tool.name} on ${on_string}: dot plot">
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
iuc
parents: 3
diff changeset
582 <filter>output_format['rplot']</filter>
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
iuc
parents: 3
diff changeset
583 </data>
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
584 </outputs>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
585 <tests>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
586 <test>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
587 <param name="ref_source" value="cached" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
588 <param name="target_2bit" value="phiX174" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
589 <param name="query" value="phiX_split.fasta" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
590 <param name="strand" value="--strand=both" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
591 <param name="format" value="general_def" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
592 <output name="output" value="test1.out" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
593 </test>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
594 <test>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
595 <param name="ref_source" value="history" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
596 <param name="target" value="phiX_split.fasta" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
597 <param name="query" value="phiX.fasta" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
598 <param name="strand" value="--strand=both" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
599 <param name="format" value="general_def" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
600 <output name="output" value="test2.out" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
601 </test>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
602 <test>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
603 <param name="ref_source" value="history" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
604 <param name="target" value="phiX_split.fasta" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
605 <param name="query" value="phiX.fasta" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
606 <param name="strand" value="--strand=both" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
607 <param name="score_file" value="score_file.txt" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
608 <param name="format" value="general_def" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
609 <output name="output" value="test3.out" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
610 </test>
3
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
611 <test>
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
612 <param name="ref_source" value="history" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
613 <param name="target" value="chrM_mouse.fa.gz" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
614 <param name="query" value="chrM_human.fa.gz" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
615 <param name="strand" value="--strand=both" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
616 <param name="format" value="blastn" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
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617 <output name="output" value="test4.out" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
618 </test>
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
619 <test>
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
620 <param name="ref_source" value="history" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
621 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
622 <param name="query" ftype="fastq.bz2" value="chrM_mouse.fq.bz2" />
4
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iuc
parents: 3
diff changeset
623 <param name="traceback" value="83886080" />
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iuc
parents: 3
diff changeset
624 <param name="word" value="28" />
3
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
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625 <param name="strand" value="--strand=both" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
626 <param name="format" value="blastn" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
627 <output name="output" value="test5.out" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
628 </test>
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
629 <test>
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
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630 <param name="ref_source" value="history" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
631 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
632 <param name="query" ftype="fastq.gz" value="chrM_mouse.fq.gz" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
633 <param name="strand" value="--strand=both" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
634 <param name="format" value="blastn" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
635 <output name="output" value="test5.out" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
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diff changeset
636 </test>
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
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637 <test>
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
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638 <param name="ref_source" value="history" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
639 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
640 <param name="query" ftype="fastq" value="chrM_mouse.fq" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
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641 <param name="strand" value="--strand=both" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
642 <param name="format" value="blastn" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
643 <output name="output" value="test5.out" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
644 </test>
2
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645 </tests>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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parents:
diff changeset
646
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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diff changeset
647 <help><![CDATA[
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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648
4
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parents: 3
diff changeset
649 **What is does**
2
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650
4
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diff changeset
651 LASTZ is designed to preprocess one sequence or set of sequences (which we collectively call the *TARGET*) and then align several *QUERY* sequences to it. It was developed by `Bob Harris <http://www.bx.psu.edu/~rsharris/>`_ in the lab of Webb Miller at Penn State.
2
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652
4
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parents: 3
diff changeset
653 .. class:: infomark
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654
4
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655 **Read documentation** before proceeding. LASTZ is a complex tool with many parameter options. Fortunately, there is a `great manual <https://lastz.github.io/lastz/>`_ maintained by its author. Default parameters may be sufficient to obtain the initial idea about how similar your sequences are, but to produce reliable alignments you may need to tweak the parameters. So RTFM!
2
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diff changeset
656
4
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parents: 3
diff changeset
657 .. class:: warningmark
2
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diff changeset
658
4
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parents: 3
diff changeset
659 Galaxy version of LASTZ sets **--ambiguous=iupac** as default (see **Scoring** section). This prevents LASTZ from erroring out if one of the DNA inputrs contains "non-strandard" nucleotides.
2
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diff changeset
660
4
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parents: 3
diff changeset
661 **About LASTZ parameters**
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662
4
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663 Galaxy's version of LASTZ has nine parameter sections (*Where to look*, *Scoring*, *Seeding*, *HSPs*, *Chaining*, *Gapped extension*, *Filtering*, *Interpolation*, and *Output*). These sections closely follow parameter description in the `manual <https://lastz.github.io/lastz/#syntax>`_.
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664
4
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diff changeset
665 **Defaults**
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
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666
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diff changeset
667 here are defaults for some of the most important parameters::
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668
4
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diff changeset
669 --seed=<pattern> set seed pattern (12of19, 14of22, or general pattern)
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diff changeset
670 (default is 1110100110010101111)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
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671 SEE "Seeding" SECTION -> "Select seed type"
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672
4
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673 --[no]transition allow (or don't) one transition in a seed hit
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diff changeset
674 (by default a transition is allowed)
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diff changeset
675 SEE "Seeding" SECTION -> "Allow transitions"
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676
4
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diff changeset
677 --[no]chain perform chaining
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
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678 (by default no chaining is performed)
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diff changeset
679 SEE "Chaining" SECTION
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parents: 3
diff changeset
680
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parents: 3
diff changeset
681 --[no]gapped perform gapped alignment (instead of gap-free)
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diff changeset
682 (by default gapped alignment is performed)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
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diff changeset
683 SEE "Gapped extension" SECTION
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684
4
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diff changeset
685 --strand=both search both strands
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686 --strand=plus search + strand only (matching strand of query spec)
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687 (by default both strands are searched)
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688 SEE "Where to look" SECTION
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689
4
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690 --scores=<file> read substitution and gap scores from a file
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691 SEE "Scoring" SECTION
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692
4
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693 --xdrop=<score> set x-drop threshold (default is 10sub[A][A])
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694 SEE "HSPs" SECTION
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695
4
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696 --ydrop=<score> set y-drop threshold (default is open+300extend)
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697 SEE "Gapped extension" SECTION
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698
4
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699 --hspthresh=<score> set threshold for high scoring pairs (default is 3000)
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700 ungapped extensions scoring lower are discarded
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701 <score> can also be a percentage or base count
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
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702 SEE "HSPs" SECTION
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703
4
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
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704 --gappedthresh=<score> set threshold for gapped alignments
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
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705 gapped extensions scoring lower are discarded
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
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706 <score> can also be a percentage or base count
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
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707 (default is to use same value as --hspthresh)
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708 SEE "Gapped extension" SECTION
2
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709
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710
4
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711 **Substitution matrix**
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712
4
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713 By default the HOXD70 substitution scores are used (from `Chiaromonte et al. 2002 <https://www.ncbi.nlm.nih.gov/pubmed/11928468>`_)::
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714
4
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715 bad_score = X:-1000 # used for sub['X'][*] and sub[*]['X']
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd
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716 fill_score = -100 # used when sub[*][*] is not defined
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717 gap_open_penalty = 400
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718 gap_extend_penalty = 30
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719
4
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720 A C G T
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721 A 91 -114 -31 -123
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722 C -114 100 -125 -31
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723 G -31 -125 100 -114
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724 T -123 -31 -114 91
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725
4
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726 Matrix can be supplied as an input to **Read the substitution scores** parameter in *Scoring* section. Substitution matrix can be inferred from your data using another LASTZ-based tool (LASTZ_D: Infer substitution scores).
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727
4
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728 **Output**
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729
4
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730 This version of LASTZ produces one output by default: a BAM alignment file. Other formats as well as a Dot Plot can be configured in *Output* section. This incarnation of LASTZ produces outputs without comment line starting with '#'. To learn identity of each column, consult `formats section of LASTZ manual <https://lastz.github.io/lastz/#formats>`_.
2
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731
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732 ]]>
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733 </help>
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734 <expand macro="citations"/>
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735 </tool>