Mercurial > repos > iuc > nanoplot
annotate nanoplot.xml @ 5:a3c4fe6f49ab draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
author | iuc |
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date | Thu, 16 Jun 2022 20:08:15 +0000 |
parents | edbb6c5028f5 |
children | 0f1c34698076 |
rev | line source |
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5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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1 <tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy1" profile="20.05"> |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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diff
changeset
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2 <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description> |
2
acd337269171
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
iuc
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changeset
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3 <macros> |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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4 <token name="@TOOL_VERSION@">1.36.2</token> |
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acd337269171
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
iuc
parents:
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diff
changeset
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5 </macros> |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
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6 <requirements> |
2
acd337269171
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
iuc
parents:
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changeset
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7 <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement> |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
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8 </requirements> |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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9 <stdio> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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10 <regex match="kaleido problem" source="stderr" level="fatal" description="No static plots are saved due to some kaleido problem" /> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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changeset
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11 </stdio> |
2
acd337269171
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
iuc
parents:
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changeset
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12 <version_command>NanoPlot --version</version_command> |
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645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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changeset
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13 <command detect_errors="exit_code"><![CDATA[ |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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diff
changeset
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14 ## set TMPDIR if not already set by admin |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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15 ## otherwise kalleido fails with `Less than 64MB of free space in temporary directory for shared memory files: 0` |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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16 ## export TMPDIR=\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR}; |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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diff
changeset
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17 |
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645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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changeset
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18 #set $myfiles = $mode.reads.files |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
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19 #set reads_temp = [] |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
changeset
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20 #if $mode.choice == 'combined': |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
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21 #for $i, $f in enumerate($myfiles) |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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22 #if $f.ext.startswith("fastq"): |
3
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
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23 #set $extension = 'fastq' |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
changeset
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24 #else |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
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25 #set $extension = $f.ext |
3
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
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26 #end if |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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27 #if $f.ext.endswith(".gz"): |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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28 #set $f = $extension + ".gz" |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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29 #else if $f.ext.endswith(".bz"): |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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30 #set $extension = $extension + "bz2" |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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changeset
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31 #end if |
3
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
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32 ln -s '$f' './read_${i}.$extension' && |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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33 #if "bam" in $extension |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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34 ln -s '$f.metadata.bam_index' './read_${i}.${extension}.bai' && |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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diff
changeset
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35 #end if |
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645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
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36 $reads_temp.append("read_" + str($i) + "." + str($extension)) |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
changeset
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37 #end for |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
changeset
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38 #else |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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39 #if $myfiles.ext.startswith("fastq"): |
3
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
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40 #set $extension = 'fastq' |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
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41 #else |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
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42 #set $extension = $myfiles.ext |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
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43 #end if |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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44 #if $myfiles.ext.endswith(".gz"): |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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45 #set $extension = $extension + ".gz" |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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46 #else if $myfiles.ext.endswith(".bz"): |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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47 #set $extension = $extension + "bz2" |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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48 #end if |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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49 ln -s '$myfiles' './read.$extension' && |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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50 #if "bam" in $extension |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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51 ln -s '$myfiles.metadata.bam_index' './read.${extension}.bai' && |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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52 #end if |
3
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
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53 $reads_temp.append("read." + str($extension)) |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
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54 #end if |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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55 |
3
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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56 NanoPlot |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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57 --threads \${GALAXY_SLOTS:-4} |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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58 --tsv_stats |
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645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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59 --$mode.reads.type ${' '.join($reads_temp)} |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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60 #if $filter.maxlength |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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61 --maxlength $filter.maxlength |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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62 #end if |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
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63 #if $filter.minlength |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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64 --minlength $filter.minlength |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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65 #end if |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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66 #if $filter.downsample |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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67 --downsample $filter.downsample |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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68 #end if |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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69 #if $filter.minqual |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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70 --minqual $filter.minqual |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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71 #end if |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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72 #if $filter.runtime_until |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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73 -- $filter.runtime_until |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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74 #end if |
3
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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75 #if $filter.readtype |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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76 --readtype $filter.readtype |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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77 #end if |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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78 #if $customization.color |
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79 --color $customization.color |
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80 #end if |
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81 #if $customization.plots |
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82 --plots ${str($customization.plots).replace(',', ' ')} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
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83 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
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84 $filter.drop_outliers |
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85 $filter.loglength |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
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86 $filter.percentqual |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
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87 $filter.alength |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
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88 $filter.barcoded |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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89 $filter.no_supplementary |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
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90 $customization.N50 |
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91 -o '.' |
5
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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92 && >&2 cat *log |
3
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93 ]]></command> |
0
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94 <inputs> |
3
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95 <conditional name="mode"> |
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96 <param name="choice" type="select" label="Select multifile mode" help="When supplying multiple files, batch mode will run NanoPlot on each file separately, while combined mode will run NanoPlot once on all the reads together. When only supplying a single input file, this setting does not matter."> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
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97 <option value="batch" selected="true">batch</option> |
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98 <option value="combined">combined</option> |
0
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99 </param> |
3
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100 <when value="batch"> |
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101 <conditional name="reads"> |
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102 <param name="type" type="select" label="Type of the file(s) to work on"> |
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103 <option value="fastq" selected="true">fastq</option> |
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104 <option value="fasta">fasta</option> |
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105 <option value="fastq_rich">fastq_rich</option> |
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106 <option value="fastq_minimal">fastq_minimal</option> |
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107 <option value="summary">summary</option> |
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108 <option value="bam">bam</option> |
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109 <option value="cram">cram</option> |
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110 </param> |
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111 <when value="fastq"> |
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112 <param type="data" argument="--fastq" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"/> |
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113 </when> |
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114 <when value="fasta"> |
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115 <param type="data" argument="--fasta" name="files" format="fasta,fasta.gz,vcf_bgzip"/> |
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116 </when> |
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117 <when value="fastq_rich"> |
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118 <param type="data" argument="--fastq_rich" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"/> |
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119 </when> |
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120 <when value="fastq_minimal"> |
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121 <param type="data" argument="--fastq_minimal" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"/> |
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122 </when> |
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123 <when value="summary"> |
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124 <param type="data" argument="--summary" name="files" format="txt,zip"/> |
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125 </when> |
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126 <when value="bam"> |
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127 <param type="data" argument="--bam" name="files" format="bam"/> |
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128 </when> |
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129 <when value="cram"> |
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130 <param type="data" argument="--cram" name="files" format="cram"/> |
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131 </when> |
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132 </conditional> |
0
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133 </when> |
3
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134 <when value="combined"> |
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135 <conditional name="reads"> |
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136 <param name="type" type="select" label="Type of the file(s) to work on"> |
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137 <option value="fastq" selected="true">fastq</option> |
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138 <option value="fasta">fasta</option> |
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139 <option value="fastq_rich">fastq_rich</option> |
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140 <option value="fastq_minimal">fastq_minimal</option> |
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141 <option value="summary">summary</option> |
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142 <option value="bam">bam</option> |
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143 <option value="cram">cram</option> |
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144 </param> |
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145 <when value="fastq"> |
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146 <param type="data" argument="--fastq" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/> |
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147 </when> |
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148 <when value="fasta"> |
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149 <param type="data" argument="--fasta" name="files" format="fasta,fasta.gz,vcf_bgzip" multiple="true"/> |
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150 </when> |
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151 <when value="fastq_rich"> |
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152 <param type="data" argument="--fastq_rich" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/> |
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153 </when> |
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154 <when value="fastq_minimal"> |
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155 <param type="data" argument="--fastq_minimal" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/> |
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156 </when> |
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|
157 <when value="summary"> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
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2
diff
changeset
|
158 <param type="data" argument="--summary" name="files" format="txt,zip" multiple="true"/> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
|
159 </when> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
|
160 <when value="bam"> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
|
161 <param type="data" argument="--bam" name="files" format="bam" multiple="true"/> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
|
162 </when> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
|
163 <when value="cram"> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
|
164 <param type="data" argument="--cram" name="files" format="cram" multiple="true"/> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
|
165 </when> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
2
diff
changeset
|
166 </conditional> |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
167 </when> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
168 </conditional> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
169 <section |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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170 name="filter" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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diff
changeset
|
171 title="Options for filtering or transforming input prior to plotting" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
172 expanded="false"> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
173 <param |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
174 type="integer" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
175 argument="--maxlength" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
|
176 optional="true" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
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177 label="Drop reads longer than length specified."/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
178 <param |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
179 type="integer" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
180 argument="--minlength" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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181 optional="true" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
182 label="Drop reads shorter than length specified."/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
183 <param |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
184 type="boolean" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
185 argument="--drop_outliers" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
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186 truevalue="--drop_outliers" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
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187 falsevalue="" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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188 label="Drop outlier reads with extreme long length."/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
189 <param |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
190 type="integer" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
191 argument="--downsample" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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192 optional="true" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
|
193 label="Reduce dataset to N reads by random sampling."/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
194 <param |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
195 type="boolean" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
196 argument="--loglength" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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diff
changeset
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197 truevalue="--loglength" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
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198 falsevalue="" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
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199 label="Logarithmic scaling of lengths in plots."/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
200 <param |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
201 type="boolean" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
202 argument="--percentqual" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
203 truevalue="--percentqual" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
204 falsevalue="" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
205 label="Use qualities as theoretical percent identities."/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
206 <param |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
207 type="boolean" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
208 argument="--alength" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
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209 truevalue="--alength" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
210 falsevalue="" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
211 label="Use aligned read lengths rather than sequenced length (bam mode)."/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
212 <param |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
213 type="integer" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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214 argument="--minqual" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
215 optional="true" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
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216 label="Drop reads with an average quality lower than specified."/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
217 <param |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
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218 type="integer" |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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4
diff
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219 argument="--runtime_until" |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
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220 optional="true" |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
|
221 label="Only take the N first hours of a run"/> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
|
222 <param |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
223 type="select" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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224 argument="--readtype" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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225 optional="true" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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226 label="Which read type to extract information about from summary."> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
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227 <option value="1D">1D</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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228 <option value="2D">2D</option> |
db1eeffba23e
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iuc
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changeset
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229 <option value="1D2">1D2</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
230 </param> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
231 <param |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
232 type="boolean" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
233 argument="--barcoded" |
db1eeffba23e
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iuc
parents:
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changeset
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234 truevalue="--barcoded" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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235 falsevalue="" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
236 label="Use if you want to split the summary file by barcode."/> |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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237 <param |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
|
238 type="boolean" |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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239 argument="--no_supplementary" |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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240 truevalue="--no_supplementary" |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
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241 falsevalue="" |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
|
242 label="Use if you want to remove supplementary alignments"/> |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
|
243 </section> |
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parents:
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changeset
|
244 <section |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
|
245 name="customization" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
246 title="Options for customizing the plots created" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
247 expanded="false"> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
248 <param |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
249 type="select" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
250 argument="--color" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
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251 optional="true" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
252 label="Specify a color for the plots."> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
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253 <option value="aliceblue">aliceblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
254 <option value="antiquewhite">antiquewhite</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
255 <option value="aqua">aqua</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
256 <option value="aquamarine">aquamarine</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
257 <option value="azure">azure</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
258 <option value="beige">beige</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
259 <option value="bisque">bisque</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
260 <option value="black">black</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
261 <option value="blanchedalmond">blanchedalmond</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
262 <option value="blue">blue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
263 <option value="blueviolet">blueviolet</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
264 <option value="brown">brown</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
265 <option value="burlywood">burlywood</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
266 <option value="cadetblue">cadetblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
267 <option value="chartreuse">chartreuse</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
268 <option value="chocolate">chocolate</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
269 <option value="coral">coral</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
270 <option value="cornflowerblue">cornflowerblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
271 <option value="cornsilk">cornsilk</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
272 <option value="crimson">crimson</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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273 <option value="cyan">cyan</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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274 <option value="darkblue">darkblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
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275 <option value="darkcyan">darkcyan</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
|
276 <option value="darkgoldenrod">darkgoldenrod</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
277 <option value="darkgray">darkgray</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
278 <option value="darkgreen">darkgreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
279 <option value="darkgrey">darkgrey</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
280 <option value="darkkhaki">darkkhaki</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
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281 <option value="darkmagenta">darkmagenta</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
282 <option value="darkolivegreen">darkolivegreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
283 <option value="darkorange">darkorange</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
284 <option value="darkorchid">darkorchid</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
285 <option value="darkred">darkred</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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286 <option value="darksalmon">darksalmon</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
287 <option value="darkseagreen">darkseagreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
288 <option value="darkslateblue">darkslateblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
289 <option value="darkslategray">darkslategray</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
290 <option value="darkslategrey">darkslategrey</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
291 <option value="darkturquoise">darkturquoise</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
292 <option value="darkviolet">darkviolet</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
293 <option value="deeppink">deeppink</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
294 <option value="deepskyblue">deepskyblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
295 <option value="dimgray">dimgray</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
296 <option value="dimgrey">dimgrey</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
297 <option value="dodgerblue">dodgerblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
298 <option value="firebrick">firebrick</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
299 <option value="floralwhite">floralwhite</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
300 <option value="forestgreen">forestgreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
301 <option value="fuchsia">fuchsia</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
302 <option value="gainsboro">gainsboro</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
303 <option value="ghostwhite">ghostwhite</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
304 <option value="goldenrod">goldenrod</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
305 <option value="gold">gold</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
306 <option value="gray">gray</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
307 <option value="green">green</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
308 <option value="greenyellow">greenyellow</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
309 <option value="grey">grey</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
310 <option value="honeydew">honeydew</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
311 <option value="hotpink">hotpink</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
312 <option value="indianred">indianred</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
313 <option value="indigo">indigo</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
314 <option value="ivory">ivory</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
315 <option value="khaki">khaki</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
316 <option value="lavenderblush">lavenderblush</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
317 <option value="lavender">lavender</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
318 <option value="lawngreen">lawngreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
319 <option value="lemonchiffon">lemonchiffon</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
320 <option value="lightblue">lightblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
321 <option value="lightcoral">lightcoral</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
322 <option value="lightcyan">lightcyan</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
323 <option value="lightgoldenrodyellow">lightgoldenrodyellow</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
324 <option value="lightgray">lightgray</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
325 <option value="lightgreen">lightgreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
326 <option value="lightgrey">lightgrey</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
327 <option value="lightpink">lightpink</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
328 <option value="lightsalmon">lightsalmon</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
329 <option value="lightseagreen">lightseagreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
330 <option value="lightskyblue">lightskyblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
331 <option value="lightslategray">lightslategray</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
332 <option value="lightslategrey">lightslategrey</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
333 <option value="lightsteelblue">lightsteelblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
334 <option value="lightyellow">lightyellow</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
335 <option value="limegreen">limegreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
336 <option value="lime">lime</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
337 <option value="linen">linen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
338 <option value="magenta">magenta</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
339 <option value="maroon">maroon</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
340 <option value="mediumaquamarine">mediumaquamarine</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
341 <option value="mediumblue">mediumblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
342 <option value="mediumorchid">mediumorchid</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
343 <option value="mediumpurple">mediumpurple</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
344 <option value="mediumseagreen">mediumseagreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
345 <option value="mediumslateblue">mediumslateblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
346 <option value="mediumspringgreen">mediumspringgreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
347 <option value="mediumturquoise">mediumturquoise</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
348 <option value="mediumvioletred">mediumvioletred</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
349 <option value="midnightblue">midnightblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
350 <option value="mintcream">mintcream</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
351 <option value="mistyrose">mistyrose</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
352 <option value="moccasin">moccasin</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
353 <option value="navajowhite">navajowhite</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
354 <option value="navy">navy</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
355 <option value="oldlace">oldlace</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
356 <option value="olivedrab">olivedrab</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
357 <option value="olive">olive</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
358 <option value="orange">orange</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
359 <option value="orangered">orangered</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
360 <option value="orchid">orchid</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
361 <option value="palegoldenrod">palegoldenrod</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
362 <option value="palegreen">palegreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
363 <option value="paleturquoise">paleturquoise</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
364 <option value="palevioletred">palevioletred</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
365 <option value="papayawhip">papayawhip</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
366 <option value="peachpuff">peachpuff</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
367 <option value="peru">peru</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
368 <option value="pink">pink</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
369 <option value="plum">plum</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
370 <option value="powderblue">powderblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
371 <option value="purple">purple</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
372 <option value="rebeccapurple">rebeccapurple</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
373 <option value="red">red</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
374 <option value="rosybrown">rosybrown</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
375 <option value="royalblue">royalblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
376 <option value="saddlebrown">saddlebrown</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
377 <option value="salmon">salmon</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
378 <option value="sandybrown">sandybrown</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
379 <option value="seagreen">seagreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
380 <option value="seashell">seashell</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
381 <option value="sienna">sienna</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
382 <option value="silver">silver</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
383 <option value="skyblue">skyblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
384 <option value="slateblue">slateblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
385 <option value="slategray">slategray</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
386 <option value="slategrey">slategrey</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
387 <option value="snow">snow</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
388 <option value="springgreen">springgreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
389 <option value="steelblue">steelblue</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
390 <option value="tan">tan</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
391 <option value="teal">teal</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
392 <option value="thistle">thistle</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
393 <option value="tomato">tomato</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
394 <option value="turquoise">turquoise</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
395 <option value="violet">violet</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
396 <option value="wheat">wheat</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
397 <option value="whitesmoke">whitesmoke</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
398 <option value="white">white</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
399 <option value="yellowgreen">yellowgreen</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
400 <option value="yellow">yellow</option> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
401 </param> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
402 <param |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
403 type="select" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
404 argument="--plots" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
405 optional="true" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
406 multiple="true" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
407 display="checkboxes" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
408 label="Specify the bivariate format of the plots."> |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
|
409 <option value="kde">kernel density estimation (kde)</option> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
4
diff
changeset
|
410 <option value="dot">dots (dot)</option> |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
411 </param> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
412 <param |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
413 type="boolean" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
414 argument="--N50" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
415 truevalue="--N50" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
416 falsevalue="" |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
417 label="Show the N50 mark in the read length histogram."/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
418 </section> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
419 </inputs> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff
changeset
|
420 <outputs> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
|
421 <data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/> |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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diff
changeset
|
422 <data name="nanostats" format="tabular" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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423 <data name="nanostats_post_filtering" format="tabular" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering" /> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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changeset
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424 <data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${tool.name} on ${on_string}: Histogram Read Length"/> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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changeset
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425 <data name="log_read_length" format="png" from_work_dir="Non_weightedLogTransformed_HistogramReadlength.png" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length"/> |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
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426 </outputs> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
|
427 <tests> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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parents:
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changeset
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428 <test> |
3
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
changeset
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429 <conditional name="mode"> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
changeset
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430 <param name="choice" value="batch"/> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
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431 <conditional name="reads"> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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432 <param name="type" value="fastq_rich"/> |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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changeset
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433 <param name="files" value="reads.fastq.gz" ftype="fastqsanger.gz"/> |
3
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
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diff
changeset
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434 </conditional> |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
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435 </conditional> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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changeset
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436 <section name="filter"> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
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437 <param name="downsample" value="800"/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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changeset
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438 </section> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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changeset
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439 <section name="customization"> |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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440 <param name="plots" value="kde"/> |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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changeset
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441 </section> |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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442 <output name="output_html" ftype="html"> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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443 <assert_contents> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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444 <has_text text="html"/> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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445 <has_text text="mean_qual"/> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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446 </assert_contents> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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447 </output> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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448 <output name="nanostats" file="NanoStats.txt" ftype="tabular"/> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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449 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="tabular"/> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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450 <output name="read_length" ftype="png" file="HistogramReadlength.png" compare="sim_size"> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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451 </output> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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452 <output name="log_read_length" ftype="png"> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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453 <assert_contents> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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454 <has_text text="PNG"/> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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455 </assert_contents> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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456 </output> |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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changeset
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457 </test> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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458 <test> |
3
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
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459 <conditional name="mode"> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
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changeset
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460 <param name="choice" value="combined"/> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
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461 <conditional name="reads"> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
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462 <param name="type" value="bam"/> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
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463 <param name="files" value="alignment.bam" ftype="bam"/> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
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464 </conditional> |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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changeset
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465 </conditional> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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changeset
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466 <section name="filter"> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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467 <param name="maxlength" value="2000"/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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changeset
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468 <param name="minlenght" value="1000"/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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changeset
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469 </section> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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changeset
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470 <section name="customization"> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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changeset
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471 <param name="color" value="yellow"/> |
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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changeset
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472 </section> |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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473 <output name="output_html" ftype="html"> |
2
acd337269171
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
iuc
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diff
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474 <assert_contents> |
acd337269171
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
iuc
parents:
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diff
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475 <has_text text="html"/> |
acd337269171
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
iuc
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476 <has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific --> |
acd337269171
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
iuc
parents:
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diff
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477 </assert_contents> |
acd337269171
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
iuc
parents:
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diff
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478 </output> |
5
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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diff
changeset
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479 <output name="read_length" ftype="png"> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
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diff
changeset
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480 <assert_contents> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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diff
changeset
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481 <has_text text="PNG"/> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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482 </assert_contents> |
a3c4fe6f49ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents:
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diff
changeset
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483 </output> |
0
db1eeffba23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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changeset
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484 </test> |
2
acd337269171
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
iuc
parents:
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diff
changeset
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485 <test><!-- test with multiple input files --> |
3
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
changeset
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486 <conditional name="mode"> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
changeset
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487 <param name="choice" value="combined"/> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
parents:
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diff
changeset
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488 <conditional name="reads"> |
645159bcee2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
iuc
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489 <param name="type" value="fasta"/> |
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490 <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta" /> |
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491 </conditional> |
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492 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
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493 <output name="output_html" ftype="html"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
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494 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
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495 <has_text text="html"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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496 <not_has_text text="Aligned read length vs Percent identity plot using dots"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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497 <has_text text="<td>9</td>"/> <!--check both files were used 4+5 reads --> |
2
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498 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
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499 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
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500 </test> |
0
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501 </tests> |
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502 <help> |
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503 <![CDATA[ |
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504 **What it does** |
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505 |
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506 NanoPlot_ is a plotting tool for long read sequencing data and alignments written by `Wouter De Coster`_ |
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507 |
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508 .. _NanoPlot: https://github.com/wdecoster/NanoPlot |
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509 .. _`Wouter De Coster`: https://github.com/wdecoster |
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510 |
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511 **Input** |
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512 |
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513 NanoPlot requires 1 or more files as input. They can either be fastq (can be generated |
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514 by albacore, guppy or MinKNOW containing additional information), fasta, sorted bam, |
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515 sorted cram or sequencing summary. |
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516 |
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517 **Output** |
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518 |
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519 NanoPlot produces different number of plots depending on the data and customizations. |
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520 A detailed view can be seen on here_. Additionally a file showing the statistics |
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521 is generated. |
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522 |
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523 .. _here: https://github.com/wdecoster/NanoPlot#plots-generated |
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524 ]]> |
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525 </help> |
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526 <citations> |
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527 <citation type="bibtex"> |
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528 @misc{githubnanoplot, author = {De Coster, Wouter}, year = {2018}, title = |
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529 {NanoPlot}, publisher = {GitHub}, journal = {GitHub repository}, url = |
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530 {https://github.com/wdecoster/NanoPlot}, }</citation> |
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531 <citation type="doi">10.1093/bioinformatics/bty149</citation> |
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532 </citations> |
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533 </tool> |