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annotate merqury.xml @ 3:f8113c25bc6b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
author iuc
date Tue, 12 Jul 2022 15:23:31 +0000
parents 589078edd230
children 09c589057ee8
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39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
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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"
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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"
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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"
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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"
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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
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16 && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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17 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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18 && ln -s '$mode.assembly_options.assembly_01' assembly.fasta
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
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19 #end if
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
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20 && merqury.sh read-db.meryl assembly.fasta ${label}
2
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
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21 #if 'log' in $output_selector
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
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22 &> $log_file
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
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23 #end if
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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24 && 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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25 && 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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26 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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27 #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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28 && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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29 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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30 && ln -s '$mode.assembly_options.assembly_01' assembly_01.fasta
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
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31 #end if
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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32 #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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33 && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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34 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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35 && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
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36 #end if
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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37 && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta ${label}
2
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
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38 #if 'log' in $output_selector
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
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39 &> $log_file
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
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40 #end if
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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41 && 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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42 && 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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43 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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44 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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45 && 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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46 && 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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47 && 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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48 && 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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49 #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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50 #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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51 && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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52 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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53 && ln -s '$mode.assembly_options.assembly_01' assembly.fasta
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
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54 #end if
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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55 && merqury.sh read-db.meryl pat.meryl mat.meryl assembly.fasta ${label}
2
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
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56 #if 'log' in $output_selector
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
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57 &> $log_file
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
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58 #end if
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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59 && 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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60 && 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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61 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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62 #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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63 && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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64 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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65 && ln -s '$mode.assembly_options.assembly_01' assembly_01.fasta
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
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66 #end if
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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67 #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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68 && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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69 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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70 && ln -s '$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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71 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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72 && merqury.sh read-db.meryl pat.meryl mat.meryl assembly_01.fasta assembly_02.fasta ${label}
2
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
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73 #if 'log' in $output_selector
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
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74 &> $log_file
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
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75 #end if
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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76 && mv ${label}* output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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77 && 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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78 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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79 #end if
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
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80
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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81 #if $output_add_headers:
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
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82 && sed -i '1s/^/assembly\tk-mer set\tsolid k-mers in assembly\tsolid k-mers in reads\tcompleteness %\n/'
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
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diff changeset
83 'output_files/${label}.completeness.stats'
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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parents: 2
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84 && sed -i '1s/^/assembly\tunique k-mers\tcommon k-mers\tQV\terror rate\n/'
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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parents: 2
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85 'output_files/${label}.qv'
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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parents: 2
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86 #end if
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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87
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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88 ]]> </command>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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89 <inputs>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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90 <conditional name="mode">
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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91 <param name="options" type="select"
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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92 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"
iuc
parents:
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93 <option value="default">Default mode</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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94 <option value="trio">Trio mode</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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95 </param>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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96 <when value="default">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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97 <param name="meryldb_F1" type="data" format="meryldb"
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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parents: 2
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98 label="K-mer counts database"
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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diff changeset
99 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"
iuc
parents:
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100 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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101 <param name="number_assemblies" type="select"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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102 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
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103 <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
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104 <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:
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105 </param>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
106 <when value="one">
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
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107 <param name="assembly_01" type="data" format="fasta,fasta.gz"
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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108 label="Genome assembly"
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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109 help="Select the assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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110 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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111 <when value="two">
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
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112 <param name="assembly_01" type="data" format="fasta,fasta.gz"
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
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113 label="First genome assembly"
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
114 help="Select the first assembled genome (FASTA)."/>
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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parents: 2
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115 <param name="assembly_02" type="data" format="fasta,fasta.gz"
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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116 label="Second genome assembly"
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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diff changeset
117 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
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118 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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119 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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120 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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diff changeset
121 <when value='trio'>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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122 <param name="meryldb_F1" type="data" format="meryldb"
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
123 label="F1 k-mer counts"
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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diff changeset
124 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
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diff changeset
125 <param name="meryldb_PAT" type="data" format="meryldb"
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
126 label="Paternal hap-mer database"
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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diff changeset
127 help="K-mer counts of the paternal haplotype (meryldb)."/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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128 <param name="meryldb_MAT" type="data" format="meryldb"
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
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129 label="Maternal hap-mer database"
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
130 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
131 <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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132 <param name="number_assemblies" type="select"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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diff changeset
133 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
134 <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
135 <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
136 </param>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
137 <when value="one">
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
138 <param name="assembly_01" type="data" format="fasta,fasta.gz"
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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parents: 2
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139 label="Genome assembly"
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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140 help="Select the assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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141 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
142 <when value="two">
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
143 <param name="assembly_01" type="data" format="fasta,fasta.gz"
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
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144 label="First genome assembly"
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
145 help="Select the first assembled genome (FASTA)."/>
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
146 <param name="assembly_02" type="data" format="fasta,fasta.gz"
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
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147 label="Second genome assembly"
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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148 help="Select the second assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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149 </when>
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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150 </conditional>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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151 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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152 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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153 <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
154 <sanitizer invalid_char="">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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155 <valid initial="string.letters,string.digits">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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156 <add value="_" />
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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157 </valid>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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158 </sanitizer>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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159 </param>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
160 <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
161 <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
162 <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
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163 <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
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164 <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
165 <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
166 <option value="wig">WIG: hap-mer tracks</option>
2
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents: 1
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167 <option value="log">Log file</option>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
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parents: 0
diff changeset
168 </param>
3
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parents: 2
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169 <param name="output_add_headers" type="boolean" value="false" label="Add column header on tabular outputs" />
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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170 </inputs>
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171 <outputs>
1
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172 <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: BED files">
0
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173 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bed" format="bed" directory="output_files"/>
1
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174 <filter>"bed" in output_selector</filter>
0
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175 </collection>
1
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176 <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: WIG files">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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177 <discover_datasets pattern="(?P&lt;name&gt;.+)\.wig" format="wig" directory="output_files"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
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178 <filter>"wig" in output_selector</filter>
0
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179 </collection>
1
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180 <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: QV stats">
0
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181 <discover_datasets pattern="(?P&lt;name&gt;.+)\.qv" format="tabular" directory="output_files"/>
1
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182 <filter>"qv" in output_selector</filter>
0
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183 </collection>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
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184 <collection name="png_files" type="list" label="${tool.name} on ${on_string}: plots">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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185 <discover_datasets pattern="(?P&lt;name&gt;.+)\.png" format="png" directory="output_files"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
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186 <filter>"plots" in output_selector</filter>
0
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187 </collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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188 <collection name="sizes_files" type="list" label="${tool.name} on ${on_string}: size files">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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189 <discover_datasets pattern="(?P&lt;name&gt;.+)\.sizes" format="tabular" directory="output_files"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
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190 <filter>"sizes" in output_selector</filter>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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191 </collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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192 <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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193 <discover_datasets pattern="(?P&lt;name&gt;.+)\.stats" format="tabular" directory="output_files"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
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194 <filter>"stats" in output_selector</filter>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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195 </collection>
2
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
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parents: 1
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196 <data name="log_file" format="txt" label="${tool.name} on ${on_string}: log file">
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
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197 <filter>"log" in output_selector</filter>
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
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parents: 1
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198 </data>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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199 </outputs>
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200 <tests>
1
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201 <!--Test 01: trio mode-->
3
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202 <test expect_num_outputs="1">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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203 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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204 <param name="options" value="trio"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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205 <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
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206 <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
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207 <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
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diff changeset
208 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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209 <param name="number_assemblies" value="one"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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210 <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"
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211 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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212 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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213 <param name="label" value="output_01"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
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parents: 0
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214 <param name="output_selector" value="sizes"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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215 <output_collection name="sizes_files" type="list" count="2">
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diff changeset
216 <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"
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217 </output_collection>
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218 </test>
3
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parents: 2
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219 <!--Test 02: standard mode with tabular headers -->
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220 <test expect_num_outputs="6">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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221 <conditional name="mode">
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222 <param name="options" value="default"/>
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223 <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"
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diff changeset
224 <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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225 <param name="number_assemblies" value="one"/>
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226 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
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227 </conditional>
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228 </conditional>
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229 <param name="label" value="output_02"/>
3
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230 <param name="output_selector" value="stats,plots,bed,sizes,qv,wig"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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231 <output_collection name="png_files" type="list" count="6">
3
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232 <element name="output_02.assembly.spectra-cn.fl">
0
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233 <assert_contents>
1
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parents: 0
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234 <has_size value="71874" delta="100"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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235 </assert_contents>
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236 </element>
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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parents: 2
diff changeset
237 <element name="output_02.assembly.spectra-cn.ln">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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238 <assert_contents>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
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parents: 0
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239 <has_size value="71888" delta="100"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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240 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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241 </element>
3
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parents: 2
diff changeset
242 <element name="output_02.assembly.spectra-cn.st">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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243 <assert_contents>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
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parents: 0
diff changeset
244 <has_size value="71123" delta="100"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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245 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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246 </element>
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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parents: 2
diff changeset
247 <element name="output_02.spectra-asm.fl">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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248 <assert_contents>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
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parents: 0
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249 <has_size value="47245" delta="100"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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250 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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251 </element>
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
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parents: 2
diff changeset
252 <element name="output_02.spectra-asm.ln">
0
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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253 <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
254 <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:
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255 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
256 </element>
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
257 <element name="output_02.spectra-asm.st">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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258 <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
259 <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
260 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
261 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
262 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
263 <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
264 <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
265 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
266 <output_collection name="qv_files" type="list" count="2">
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
267 <!--
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
268 Had to remove this to pass test due to planemo errors
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
269 <element name="output_02.assembly" ftype="tabular"/>
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
270 -->
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
271 <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
272 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
273 <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
274 <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
275 <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
276 <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
277 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
278 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
279 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
280 <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
281 <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:
diff changeset
282 <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
283 <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
284 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
285 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
286 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
287 </test>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
288 <!--Test 03: Standard mode two assemblies-->
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
289 <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
290 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
291 <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
292 <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
293 <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
294 <param name="number_assemblies" value="two"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
295 <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
296 <param name="assembly_02" value="assembly_02.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
297 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
298 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
299 <param name="label" value="output_03"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
300 <param name="output_selector" value="qv,stats"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
301 <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
302 <element name="output_03.completeness" file="output_03.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
303 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
304 <output_collection name="qv_files" type="list" count="3">
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
305 <!-- Had to remove these to pass test due to planemo errors: "no file to compare"
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
306 <element name="output_03.assembly_01" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
307 <element name="output_03.assembly_02" ftype="tabular"/>
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
308 -->
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
309 <element name="output_03" file="output_03_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
310 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
311 </test>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
312 <!--Test 04: trio mode two assemblies-->
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
313 <test expect_num_outputs="1">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
314 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
315 <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
316 <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
317 <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
318 <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
319 <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
320 <param name="number_assemblies" value="two"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
321 <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
322 <param name="assembly_02" value="assembly_02.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
323 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
324 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
325 <param name="label" value="output_04"/>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
326 <param name="output_selector" value="qv"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
327 <output_collection name="qv_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
328 <element name="output_04" file="output_04_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
329 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
330 </test>
2
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents: 1
diff changeset
331 <!--Test 05: log file-->
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents: 1
diff changeset
332 <test expect_num_outputs="2">
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents: 1
diff changeset
333 <conditional name="mode">
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents: 1
diff changeset
334 <param name="options" value="trio"/>
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents: 1
diff changeset
335 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents: 1
diff changeset
336 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents: 1
diff changeset
337 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents: 1
diff changeset
338 <conditional name="assembly_options">
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents: 1
diff changeset
339 <param name="number_assemblies" value="two"/>
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
iuc
parents: 1
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340 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
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341 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
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342 </conditional>
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343 </conditional>
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344 <param name="label" value="output_05"/>
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345 <param name="output_selector" value="qv,log"/>
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346 <output_collection name="qv_files" type="list" count="1">
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347 <element name="output_05" file="output_04_qv.tabular" ftype="tabular"/>
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348 </output_collection>
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349 <output name="log_file" file="output_05_log.txt" ftype="txt" lines_diff='4'/>
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350 </test>
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351 <!--Test 06: standard mode with tabular headers -->
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352 <test expect_num_outputs="2">
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353 <conditional name="mode">
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354 <param name="options" value="default"/>
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355 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
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356 <conditional name="assembly_options">
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357 <param name="number_assemblies" value="one"/>
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358 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
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359 </conditional>
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360 </conditional>
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361 <param name="label" value="output_06"/>
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362 <param name="output_selector" value="stats,qv"/>
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363 <param name="output_add_headers" value="true"/>
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364 <output_collection name="stats_files" type="list" count="1">
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365 <element name="output_06.completeness" file="output_06.completeness.stats.tabular" ftype="tabular"/>
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366 </output_collection>
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367 <output_collection name="qv_files" type="list" count="2">
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368 <element name="output_06" file="output_06_qv.tabular" ftype="tabular"/>
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369 </output_collection>
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370 </test>
0
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371 </tests>
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372 <help><![CDATA[
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373 .. class:: infomark
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374
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375 **Purpose**
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376
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377 Merqury allows a reference-free assembly evaluation based on efficient k-mer set operations. By comparing k-mers in a de novo
3
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378 assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness.
0
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379
3
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380 For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors.
0
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381
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382 ----
3
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383
0
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384 .. class:: infomark
3
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385
0
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386 **Input**
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387
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388 Merqury requires two types of inputs: meryldbs and the genome assemblies.
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389 There is no need to run merqury per-assemblies. If two assemblies areprovided, Merqury generates stats for each and combined.
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390
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391 ----
3
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392
0
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393 .. class:: infomark
3
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394
0
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395 **Output**
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396
3
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397 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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398
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399 You can add column headers to the ``completeness`` and ``qv`` outputs by checking the option "Add column header on tabular outputs".
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400
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401 ]]> </help>
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402 <expand macro="citations"/>
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403 </tool>