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annotate merqury.xml @ 4:09c589057ee8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4
author iuc
date Thu, 10 Aug 2023 22:57:52 +0000
parents f8113c25bc6b
children eb7b00ec347d
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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"
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"
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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
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"
iuc
parents: 1
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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
parents: 1
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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
parents:
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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
parents: 2
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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"
iuc
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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
parents:
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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
parents: 1
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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"
iuc
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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
parents: 1
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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
parents: 2
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80
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
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81 #if $output_add_headers:
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
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82 && sed -i '1s/^/assembly\tk-mer set\tsolid k-mers in assembly\tsolid k-mers in reads\tcompleteness %\n/'
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
83 'output_files/${label}.completeness.stats'
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
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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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"
iuc
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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:
diff changeset
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
iuc
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
parents:
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:
diff changeset
100 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
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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:
diff changeset
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
parents:
diff changeset
110 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
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
diff changeset
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
diff changeset
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
iuc
parents: 2
diff changeset
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
parents:
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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diff changeset
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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diff changeset
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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diff changeset
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
parents:
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
parents:
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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diff changeset
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
parents: 2
diff changeset
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
iuc
parents: 2
diff changeset
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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diff changeset
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
parents:
diff changeset
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
diff changeset
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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diff changeset
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"
iuc
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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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parents: 2
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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"
iuc
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diff changeset
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"
iuc
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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
parents:
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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"
iuc
parents:
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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
diff changeset
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
diff changeset
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>
4
09c589057ee8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4
iuc
parents: 3
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167 <option value="hist">Histogram files</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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168 <option value="log">Log file</option>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
169 </param>
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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170 <param name="output_add_headers" type="boolean" value="false" label="Add column header on tabular outputs" />
0
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171 </inputs>
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172 <outputs>
1
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173 <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: BED files">
0
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174 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bed" format="bed" directory="output_files"/>
1
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175 <filter>"bed" in output_selector</filter>
0
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176 </collection>
1
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177 <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: WIG files">
0
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178 <discover_datasets pattern="(?P&lt;name&gt;.+)\.wig" format="wig" directory="output_files"/>
1
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179 <filter>"wig" in output_selector</filter>
0
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180 </collection>
1
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181 <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: QV stats">
0
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182 <discover_datasets pattern="(?P&lt;name&gt;.+)\.qv" format="tabular" directory="output_files"/>
1
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183 <filter>"qv" in output_selector</filter>
0
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184 </collection>
1
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185 <collection name="png_files" type="list" label="${tool.name} on ${on_string}: plots">
0
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186 <discover_datasets pattern="(?P&lt;name&gt;.+)\.png" format="png" directory="output_files"/>
1
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187 <filter>"plots" in output_selector</filter>
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188 </collection>
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189 <collection name="sizes_files" type="list" label="${tool.name} on ${on_string}: size files">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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190 <discover_datasets pattern="(?P&lt;name&gt;.+)\.sizes" format="tabular" directory="output_files"/>
1
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191 <filter>"sizes" in output_selector</filter>
0
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192 </collection>
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193 <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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194 <discover_datasets pattern="(?P&lt;name&gt;.+)\.stats" format="tabular" directory="output_files"/>
1
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195 <filter>"stats" in output_selector</filter>
0
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196 </collection>
2
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197 <data name="log_file" format="txt" label="${tool.name} on ${on_string}: log file">
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
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198 <filter>"log" in output_selector</filter>
589078edd230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
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199 </data>
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200 <collection name="hist_files" type="list" label="${tool.name} on ${on_string}: histograms">
09c589057ee8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4
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201 <discover_datasets pattern="(?P&lt;name&gt;.+)\.hist" format="tabular" directory="output_files"/>
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202 <filter>"hist" in output_selector</filter>
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203 </collection>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
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204 </outputs>
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205 <tests>
1
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206 <!--Test 01: trio mode-->
3
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207 <test expect_num_outputs="1">
0
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208 <conditional name="mode">
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209 <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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210 <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"
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211 <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"
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212 <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"
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213 <conditional name="assembly_options">
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214 <param name="number_assemblies" value="one"/>
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215 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
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216 </conditional>
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217 </conditional>
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218 <param name="label" value="output_01"/>
1
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219 <param name="output_selector" value="sizes"/>
0
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220 <output_collection name="sizes_files" type="list" count="2">
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221 <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/>
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222 </output_collection>
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223 </test>
3
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224 <!--Test 02: standard mode with tabular headers -->
4
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225 <test expect_num_outputs="7">
0
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226 <conditional name="mode">
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227 <param name="options" value="default"/>
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228 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
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229 <conditional name="assembly_options">
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230 <param name="number_assemblies" value="one"/>
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231 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
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232 </conditional>
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233 </conditional>
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234 <param name="label" value="output_02"/>
4
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235 <param name="output_selector" value="stats,plots,bed,sizes,qv,wig,hist"/>
0
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236 <output_collection name="png_files" type="list" count="6">
3
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237 <element name="output_02.assembly.spectra-cn.fl">
0
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238 <assert_contents>
1
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239 <has_size value="71874" delta="100"/>
0
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240 </assert_contents>
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241 </element>
3
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242 <element name="output_02.assembly.spectra-cn.ln">
0
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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
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244 <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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245 </assert_contents>
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246 </element>
3
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247 <element name="output_02.assembly.spectra-cn.st">
0
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248 <assert_contents>
1
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parents: 0
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249 <has_size value="71123" delta="100"/>
0
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250 </assert_contents>
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251 </element>
3
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diff changeset
252 <element name="output_02.spectra-asm.fl">
0
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253 <assert_contents>
1
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254 <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
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.ln">
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
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="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
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>
3
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
262 <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
parents:
diff changeset
263 <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
264 <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
265 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
266 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
267 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
268 <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
269 <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
270 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
271 <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
272 <!--
f8113c25bc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit dab8c5d9603de18548f1a5bd973ffa92b016936f
iuc
parents: 2
diff changeset
273 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
274 <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
275 -->
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
276 <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
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diff changeset
277 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
278 <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
279 <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:
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280 <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
281 <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
282 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
283 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
284 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
285 <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
286 <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
287 <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
288 <has_size value="0"/>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
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289 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
290 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
291 </output_collection>
4
09c589057ee8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4
iuc
parents: 3
diff changeset
292 <output_collection name="hist_files" type="list" count="4">
09c589057ee8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4
iuc
parents: 3
diff changeset
293 <element name="output_02.spectra-asm" file="output_02.spectra-asm.hist" ftype="tabular"/>
09c589057ee8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4
iuc
parents: 3
diff changeset
294 <element name="output_02.dist_only" file="output_02.dist_only.hist" ftype="tabular"/>
09c589057ee8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4
iuc
parents: 3
diff changeset
295 <element name="output_02.assembly.spectra-cn" file="output_02.assembly.spectra-cn.hist" ftype="tabular"/>
09c589057ee8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4
iuc
parents: 3
diff changeset
296 <element name="output_02.assembly.only" file="output_02.assembly.only.hist" ftype="tabular"/>
09c589057ee8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4
iuc
parents: 3
diff changeset
297 </output_collection>
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
298 </test>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
299 <!--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
300 <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
301 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
302 <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
303 <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
304 <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
305 <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
306 <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
307 <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
308 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
309 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
310 <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
311 <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
312 <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
313 <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
314 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
315 <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
316 <!-- 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
317 <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
318 <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
319 -->
0
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
320 <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
321 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
322 </test>
1
39edec572bae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"
iuc
parents: 0
diff changeset
323 <!--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
324 <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
325 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
326 <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
327 <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
328 <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
329 <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
330 <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
331 <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
332 <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
333 <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
334 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
335 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"
iuc
parents:
diff changeset
336 <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
337 <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
338 <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
339 <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
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340 </output_collection>
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341 </test>
2
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342 <!--Test 05: log file-->
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343 <test expect_num_outputs="2">
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344 <conditional name="mode">
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345 <param name="options" value="trio"/>
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346 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
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347 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
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348 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>
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349 <conditional name="assembly_options">
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350 <param name="number_assemblies" value="two"/>
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351 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
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352 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
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353 </conditional>
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354 </conditional>
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355 <param name="label" value="output_05"/>
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356 <param name="output_selector" value="qv,log"/>
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357 <output_collection name="qv_files" type="list" count="1">
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358 <element name="output_05" file="output_04_qv.tabular" ftype="tabular"/>
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359 </output_collection>
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360 <output name="log_file" file="output_05_log.txt" ftype="txt" lines_diff='4'/>
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361 </test>
3
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362 <!--Test 06: standard mode with tabular headers -->
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363 <test expect_num_outputs="2">
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364 <conditional name="mode">
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365 <param name="options" value="default"/>
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366 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
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367 <conditional name="assembly_options">
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368 <param name="number_assemblies" value="one"/>
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369 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
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370 </conditional>
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371 </conditional>
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372 <param name="label" value="output_06"/>
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373 <param name="output_selector" value="stats,qv"/>
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374 <param name="output_add_headers" value="true"/>
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375 <output_collection name="stats_files" type="list" count="1">
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376 <element name="output_06.completeness" file="output_06.completeness.stats.tabular" ftype="tabular"/>
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377 </output_collection>
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378 <output_collection name="qv_files" type="list" count="2">
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379 <element name="output_06" file="output_06_qv.tabular" ftype="tabular"/>
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380 </output_collection>
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381 </test>
0
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382 </tests>
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383 <help><![CDATA[
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384 .. class:: infomark
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385
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386 **Purpose**
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387
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388 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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389 assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness.
0
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390
3
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391 For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors.
0
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392
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393 ----
3
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394
0
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395 .. class:: infomark
3
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396
0
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397 **Input**
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398
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399 Merqury requires two types of inputs: meryldbs and the genome assemblies.
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400 There is no need to run merqury per-assemblies. If two assemblies areprovided, Merqury generates stats for each and combined.
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401
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402 ----
3
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403
0
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404 .. class:: infomark
3
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405
0
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406 **Output**
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407
3
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408 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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409
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410 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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411
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412 ]]> </help>
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413 <expand macro="citations"/>
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414 </tool>