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annotate merqury.xml @ 1:39edec572bae draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
author iuc
date Thu, 11 Nov 2021 16:38:42 +0000
parents 9d79beb19ac3
children 589078edd230
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39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
1 <tool id="merqury" name="Merqury" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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2 <description>evaluate the assembly quality</description>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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3 <macros>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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4 <import>macros.xml</import>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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5 </macros>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
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6 <expand macro="bio_tools"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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7 <expand macro="requirements"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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8 <version_command>merqury --version</version_command>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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9 <command detect_errors="exit_code"><![CDATA[
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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10 mkdir -p output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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11 #if $mode.options == 'default'
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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12 && mkdir -p read-db.meryl
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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13 && tar -zxf ${mode.meryldb_F1} -C read-db.meryl --strip-components=1
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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14 #if $mode.assembly_options.number_assemblies == 'one'
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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15 #if $mode.assembly_options.assembly_01.ext.endswith(".gz")
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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16 && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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17 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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18 && ln -s '$mode.assembly_options.assembly_01' assembly.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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19 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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20 && merqury.sh read-db.meryl assembly.fasta ${label}
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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21 && mv ${label}* output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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22 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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23 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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24 #if $mode.assembly_options.assembly_01.ext.endswith(".gz")
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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25 && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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26 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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27 && ln -s '$mode.assembly_options.assembly_01' assembly_01.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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28 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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29 #if $mode.assembly_options.assembly_02.ext.endswith(".gz")
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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30 && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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31 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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32 && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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33 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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34 && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta ${label}
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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35 && mv ${label}* output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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36 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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37 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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38 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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39 && mkdir -p read-db.meryl pat.meryl mat.meryl
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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40 && tar -zxf ${mode.meryldb_F1} -C read-db.meryl --strip-components=1
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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41 && tar -zxf ${mode.meryldb_PAT} -C pat.meryl --strip-components=1
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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42 && tar -zxf ${mode.meryldb_MAT} -C mat.meryl --strip-components=1
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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43 #if $mode.assembly_options.number_assemblies == 'one'
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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44 #if $mode.assembly_options.assembly_01.ext.endswith(".gz")
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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45 && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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46 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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47 && ln -s '$mode.assembly_options.assembly_01' assembly.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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48 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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49 && merqury.sh read-db.meryl pat.meryl mat.meryl assembly.fasta ${label}
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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50 && mv ${label}* output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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51 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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52 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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53 #if $mode.assembly_options.assembly_01.ext.endswith(".gz")
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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54 && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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55 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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56 && ln -s '$mode.assembly_options.assembly_01' assembly_01.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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57 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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58 #if $mode.assembly_options.assembly_02.ext.endswith(".gz")
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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59 && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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60 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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61 && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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62 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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63 && merqury.sh read-db.meryl pat.meryl mat.meryl assembly_01.fasta assembly_02.fasta ${label}
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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64 && mv ${label}* output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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65 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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66 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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67 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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68 ]]> </command>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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69 <inputs>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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70 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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71 <param name="options" type="select"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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72 label="Evaluation mode" help="Merqury allows two operational modes: default and trio mode.">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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73 <option value="default">Default mode</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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74 <option value="trio">Trio mode</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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75 </param>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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76 <when value="default">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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77 <param name="meryldb_F1" type="data" format="meryldb"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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78 label="K-mer counts database"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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79 help="Select the k-mer counts of the read set."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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80 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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81 <param name="number_assemblies" type="select"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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82 label="Number of assemblies" help="Select the number of assemblies.">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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83 <option value="one">One assembly (pseudo-haplotype or mixed-haplotype)</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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parents:
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84 <option value="two">Two assemblies (diploid)</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
85 </param>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
86 <when value="one">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
87 <param name="assembly_01" type="data" format="fasta,fasta.gz"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
88 label="Genome assembly"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
89 help="Select the assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
90 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
91 <when value="two">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
92 <param name="assembly_01" type="data" format="fasta,fasta.gz"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
93 label="First genome assembly"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
94 help="Select the first assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
95 <param name="assembly_02" type="data" format="fasta,fasta.gz"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
96 label="Second genome assembly"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
97 help="Select the second assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
98 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
99 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
100 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
101 <when value='trio'>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
102 <param name="meryldb_F1" type="data" format="meryldb"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
103 label="F1 k-mer counts"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
104 help="Select the k-mer counts of the read set (meryldb )."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
105 <param name="meryldb_PAT" type="data" format="meryldb"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
106 label="Paternal hap-mer database"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
107 help="K-mer counts of the paternal haplotype (meryldb)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
108 <param name="meryldb_MAT" type="data" format="meryldb"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
109 label="Maternal hap-mer database"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
110 help="K-mer counts of the maternal haplotype (meryldb)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
111 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
112 <param name="number_assemblies" type="select"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
113 label="Number of assemblies" help="Select the number of assemblies.">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
114 <option value="one">One assembly (pseudo-haplotype or mixed-haplotype)</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
115 <option value="two">Two assemblies (diploid)</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
116 </param>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
117 <when value="one">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
118 <param name="assembly_01" type="data" format="fasta,fasta.gz"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
119 label="Genome assembly"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
120 help="Select the assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
121 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
122 <when value="two">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
123 <param name="assembly_01" type="data" format="fasta,fasta.gz"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
124 label="First genome assembly"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
125 help="Select the first assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
126 <param name="assembly_02" type="data" format="fasta,fasta.gz"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
127 label="Second genome assembly"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
128 help="Select the second assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
129 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
130 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
131 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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132 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
133 <param name='label' type="text" value="output_merqury" label="Identification label" help="Assign an identification label.">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
134 <sanitizer invalid_char="">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
135 <valid initial="string.letters,string.digits">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
136 <add value="_" />
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
137 </valid>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
138 </sanitizer>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
139 </param>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
140 <param name="output_selector" type="select" display="checkboxes" multiple="true" optional="true" label="Output options">
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
141 <option value="qv" selected="true">QV stats</option>
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
142 <option value="plots" selected="true">Plots</option>
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
143 <option value="sizes">Size files</option>
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
144 <option value="stats" selected="true">Stats file</option>
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
145 <option value="bed">BED: hap-mer tracks</option>
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
146 <option value="wig">WIG: hap-mer tracks</option>
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
147 </param>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
148 </inputs>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
149 <outputs>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
150 <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: BED files">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
151 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bed" format="bed" directory="output_files"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
152 <filter>"bed" in output_selector</filter>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
153 </collection>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
154 <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: WIG files">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
155 <discover_datasets pattern="(?P&lt;name&gt;.+)\.wig" format="wig" directory="output_files"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
156 <filter>"wig" in output_selector</filter>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
157 </collection>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
158 <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: QV stats">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
159 <discover_datasets pattern="(?P&lt;name&gt;.+)\.qv" format="tabular" directory="output_files"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
160 <filter>"qv" in output_selector</filter>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
161 </collection>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
162 <collection name="png_files" type="list" label="${tool.name} on ${on_string}: plots">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
163 <discover_datasets pattern="(?P&lt;name&gt;.+)\.png" format="png" directory="output_files"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
164 <filter>"plots" in output_selector</filter>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
165 </collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
166 <collection name="sizes_files" type="list" label="${tool.name} on ${on_string}: size files">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
167 <discover_datasets pattern="(?P&lt;name&gt;.+)\.sizes" format="tabular" directory="output_files"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
168 <filter>"sizes" in output_selector</filter>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
169 </collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
170 <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
171 <discover_datasets pattern="(?P&lt;name&gt;.+)\.stats" format="tabular" directory="output_files"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
172 <filter>"stats" in output_selector</filter>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
173 </collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
174 </outputs>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
175 <tests>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
176 <!--Test 01: trio mode-->
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
177 <test expect_num_outputs="2">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
178 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
179 <param name="options" value="trio"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
180 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
181 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
182 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
183 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
184 <param name="number_assemblies" value="one"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
185 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
186 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
187 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
188 <param name="label" value="output_01"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
189 <param name="output_selector" value="sizes"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
190 <output_collection name="sizes_files" type="list" count="2">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
191 <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
192 <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
193 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
194 </test>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
195 <!--Test 02: standard mode-->
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
196 <test expect_num_outputs="11">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
197 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
198 <param name="options" value="default"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
199 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
200 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
201 <param name="number_assemblies" value="one"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
202 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
203 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
204 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
205 <param name="label" value="output_02"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
206 <param name="output_selector" value="qv,png,bed,wig,sizes,stats"/>
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
207 <param name="output_selector" value="plots,stats,wig,sizes,bed"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
208 <output_collection name="png_files" type="list" count="6">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
209 <element name="output_02.assembly.spectra-cn.fl" file="output_02.assembly.spectra-cn.fl.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
210 <assert_contents>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
211 <has_size value="71874" delta="100"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
212 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
213 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
214 <element name="output_02.assembly.spectra-cn.ln" file="output_02.assembly.spectra-cn.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
215 <assert_contents>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
216 <has_size value="71888" delta="100"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
217 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
218 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
219 <element name="output_02.assembly.spectra-cn.st" file="output_02.assembly.spectra-cn.st.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
220 <assert_contents>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
221 <has_size value="71123" delta="100"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
222 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
223 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
224 <element name="output_02.spectra-asm.fl" file="output_02.spectra-asm.fl.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
225 <assert_contents>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
226 <has_size value="47245" delta="100"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
227 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
228 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
229 <element name="output_02.spectra-asm.ln" file="output_02.spectra-asm.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
230 <assert_contents>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
231 <has_size value="46896" delta="100"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
232 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
233 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
234 <element name="output_02.spectra-asm.st" file="output_02.spectra-asm.st.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
235 <assert_contents>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
236 <has_size value="45945" delta="100"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
237 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
238 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
239 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
240 <output_collection name="stats_files" type="list" count="1">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
241 <element name="output_02.completeness" file="output_02.completeness.stats.tabular" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
242 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
243 <output_collection name="qv_files" type="list" count="2">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
244 <element name="output_02.assembly" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
245 <element name="output_02" file="output_02_qv.tabular" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
246 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
247 <output_collection name="wig_files" type="list" count="1">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
248 <element name="assembly_only" ftype="wig">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
249 <assert_contents>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
250 <has_size value="0"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
251 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
252 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
253 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
254 <output_collection name="bed_files" type="list" count="1">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
255 <element name="assembly_only" ftype="bed">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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256 <assert_contents>
1
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257 <has_size value="0"/>
0
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258 </assert_contents>
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259 </element>
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260 </output_collection>
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261 </test>
1
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262 <!--Test 03: Standard mode two assemblies-->
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263 <test expect_num_outputs="4">
0
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264 <conditional name="mode">
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265 <param name="options" value="default"/>
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266 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
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267 <conditional name="assembly_options">
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268 <param name="number_assemblies" value="two"/>
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269 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
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270 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
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271 </conditional>
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272 </conditional>
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273 <param name="label" value="output_03"/>
1
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274 <param name="output_selector" value="qv,stats"/>
0
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275 <output_collection name="stats_files" type="list" count="1">
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276 <element name="output_03.completeness" file="output_03.completeness.stats.tabular" ftype="tabular"/>
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277 </output_collection>
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278 <output_collection name="qv_files" type="list" count="3">
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279 <element name="output_03.assembly_01" ftype="tabular"/>
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280 <element name="output_03.assembly_02" ftype="tabular"/>
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281 <element name="output_03" file="output_03_qv.tabular" ftype="tabular"/>
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282 </output_collection>
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283 </test>
1
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284 <!--Test 04: trio mode two assemblies-->
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285 <test expect_num_outputs="1">
0
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286 <conditional name="mode">
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287 <param name="options" value="trio"/>
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288 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
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289 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
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290 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>
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291 <conditional name="assembly_options">
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292 <param name="number_assemblies" value="two"/>
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293 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
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294 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
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295 </conditional>
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296 </conditional>
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297 <param name="label" value="output_04"/>
1
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298 <param name="output_selector" value="qv"/>
0
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299 <output_collection name="qv_files" type="list" count="1">
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300 <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/>
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301 </output_collection>
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302 </test>
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303 </tests>
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304 <help><![CDATA[
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305 .. class:: infomark
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306
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307 **Purpose**
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308
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309 Merqury allows a reference-free assembly evaluation based on efficient k-mer set operations. By comparing k-mers in a de novo
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310 assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness.
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311
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312 For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors.
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313
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314 ----
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315
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316 .. class:: infomark
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317
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318 **Input**
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319
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320 Merqury requires two types of inputs: meryldbs and the genome assemblies.
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321 There is no need to run merqury per-assemblies. If two assemblies areprovided, Merqury generates stats for each and combined.
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322
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323 ----
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324
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325 .. class:: infomark
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326
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327 **Output**
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328
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329 The generated metrics include consensus quality and k-mer completeness, and when parental genomic sequences are available (either assembled or unassembled), Merqury can output haplotype completeness, phase block statistics, switch error rates, and visual representations of phase consistency for the child’s genome. This includes TDF (or BED) features that can be displayed in a genome browser for visualizing the presence of k-mer classes across a genome (e.g., the k-mers inherited from a parental genome).
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330
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331 ]]> </help>
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332 <expand macro="citations"/>
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333 </tool>