Mercurial > repos > iuc > poretools_squiggle
annotate poretools_squiggle.xml @ 1:34553d0caa5e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
| author | iuc |
|---|---|
| date | Sun, 19 Jan 2020 09:09:16 -0500 |
| parents | ce8af9373061 |
| children | 26e6c9362b7b |
| rev | line source |
|---|---|
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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1 <?xml version="1.0"?> |
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1
34553d0caa5e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
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2 <tool id="poretools_squiggle" name="Plot signals" version="@VERSION@.1" profile="@profile@"> |
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0
ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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3 <description>for nanopore reads</description> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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4 <macros> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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5 <import>macros.xml</import> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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6 </macros> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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7 <expand macro="requirements" /> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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8 <command detect_errors="aggressive"> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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9 <![CDATA[ |
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1
34553d0caa5e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
0
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10 @MPLBACKEND@ |
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34553d0caa5e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
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diff
changeset
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11 poretools squiggle '$input' --saveas $extension --num-facets $num_facets $theme_bw |
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0
ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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12 ]]> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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13 </command> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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14 <inputs> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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15 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" /> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
16 <expand macro="plot_options" /> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
17 <param name="num_facets" argument="--num-facets" type="integer" value="6" label="Number of plot facets" /> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
18 </inputs> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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19 <outputs> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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20 <data format="txt" name="output"> |
|
ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
21 <discover_datasets pattern="__designation_and_ext__" directory="." visible="true" /> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
22 </data> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
23 </outputs> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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24 <tests> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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25 <test> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
26 <expand macro="test_input" /> |
|
ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
27 <param name="extension" value="png" /> |
|
ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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28 <output name="output"> |
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1
34553d0caa5e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
0
diff
changeset
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29 <discovered_dataset designation="2016_3_4_3507_1_ch128_read430_strand.fast5" file="poretools-squiggle-out1-1.png" compare="sim_size" /> |
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34553d0caa5e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
0
diff
changeset
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30 <discovered_dataset designation="2016_3_4_3507_1_ch128_read95_strand.fast5" file="poretools-squiggle-out1-2.png" compare="sim_size" /> |
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0
ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
31 </output> |
|
ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
32 </test> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
33 <test> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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34 <expand macro="test_input" /> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
35 <param name="extension" value="pdf" /> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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36 <output name="output"> |
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1
34553d0caa5e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
0
diff
changeset
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37 <discovered_dataset designation="2016_3_4_3507_1_ch128_read430_strand.fast5" file="poretools-squiggle-out1-1.pdf" compare="sim_size" /> |
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34553d0caa5e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
0
diff
changeset
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38 <discovered_dataset designation="2016_3_4_3507_1_ch128_read95_strand.fast5" file="poretools-squiggle-out1-2.pdf" compare="sim_size" /> |
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0
ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
|
39 </output> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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40 </test> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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41 </tests> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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42 <help> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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43 Plot the observed signals for FAST5 reads. |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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44 </help> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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45 <expand macro="citations" /> |
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ce8af9373061
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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46 </tool> |