Mercurial > repos > iuc > poretools_yield_plot
annotate poretools_yield_plot.xml @ 2:c5c5a3e84989 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit 506782d1e671505617ff539e6811fcdcc2c02cd5
author | iuc |
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date | Fri, 27 Sep 2024 07:46:01 +0000 |
parents | ca22d8497db5 |
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2
c5c5a3e84989
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit 506782d1e671505617ff539e6811fcdcc2c02cd5
iuc
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1 <tool id="poretools_yield_plot" name="Collector’s curve" version="@VERSION@.1" profile="@PROFILE@"> |
0
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
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2 <description>of sequencing yield over time</description> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
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changeset
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3 <macros> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
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changeset
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4 <import>macros.xml</import> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
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5 </macros> |
2
c5c5a3e84989
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit 506782d1e671505617ff539e6811fcdcc2c02cd5
iuc
parents:
1
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changeset
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6 <expand macro="bio_tools"/> |
1
ca22d8497db5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
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7 <expand macro="requirements"/> |
0
64a83664b814
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"> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
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9 <![CDATA[ |
1
ca22d8497db5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
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10 @MPLBACKEND@ |
ca22d8497db5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
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11 poretools yield_plot '$input' --saveas plot.$extension --plot-type $plot_type |
ca22d8497db5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
0
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12 $theme_bw |
ca22d8497db5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
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13 #if $skip != '0': |
ca22d8497db5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
0
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14 --skip $skip |
ca22d8497db5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
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0
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15 #end if |
ca22d8497db5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
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16 && mv plot.$extension '$output' |
0
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
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17 ]]> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
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18 </command> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
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19 <inputs> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
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20 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" /> |
2
c5c5a3e84989
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit 506782d1e671505617ff539e6811fcdcc2c02cd5
iuc
parents:
1
diff
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21 <param argument="--plot-type" type="select" label="Plot reads or base pairs"> |
0
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
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22 <option value="reads">Reads</option> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
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changeset
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23 <option value="basepairs">Base pairs</option> |
64a83664b814
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 </param> |
1
ca22d8497db5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
0
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25 <param argument="--skip" type="integer" min="1" value="1" label="Plot only every nth point" help="Increases performance at the cost of resolution." /> |
0
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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26 <expand macro="plot_options" /> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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27 </inputs> |
64a83664b814
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 <outputs> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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29 <expand macro="image_output" /> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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30 </outputs> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
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31 <tests> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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32 <test> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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33 <expand macro="test_input" /> |
64a83664b814
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 <param name="extension" value="png" /> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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35 <param name="plot_type" value="reads" /> |
1
ca22d8497db5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
0
diff
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36 <output name="output" file="poretools-yield-plot-out1.png" ftype="png" compare="sim_size" /> |
0
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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37 </test> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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38 <test> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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39 <expand macro="test_input" /> |
64a83664b814
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 <param name="extension" value="svg" /> |
64a83664b814
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 <param name="plot_type" value="basepairs" /> |
1
ca22d8497db5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents:
0
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42 <output name="output" file="poretools-yield-plot-out2.svg" ftype="svg" lines_diff="50" /> |
0
64a83664b814
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 </test> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
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44 </tests> |
64a83664b814
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 <help> |
64a83664b814
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 Create a collector’s curve reflecting the sequencing yield over time. |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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47 </help> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
changeset
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48 <expand macro="citations" /> |
64a83664b814
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff
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49 </tool> |