Mercurial > repos > iuc > poretools_yield_plot

annotate poretools_yield_plot.xml @ 1:b17593289ad0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
author iuc
date Sun, 19 Jan 2020 14:05:14 +0000
parents a8c8a7354ab7
children d4bbe0275728
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
1
b17593289ad0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents: 0
diff changeset
2 <tool id="poretools_yield_plot" name="Collector’s curve" version="@VERSION@.1">
0
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
3 <description>of sequencing yield over time</description>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
4 <macros>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
5 <import>macros.xml</import>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
6 </macros>
1
b17593289ad0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents: 0
diff changeset
7 <expand macro="requirements"/>
0
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
8 <command detect_errors="aggressive">
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
9 <![CDATA[
1
b17593289ad0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents: 0
diff changeset
10 @MPLBACKEND@
b17593289ad0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents: 0
diff changeset
11 poretools yield_plot '$input' --saveas plot.$extension --plot-type $plot_type
b17593289ad0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents: 0
diff changeset
12 $theme_bw
b17593289ad0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents: 0
diff changeset
13 #if $skip != '0':
b17593289ad0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents: 0
diff changeset
14 --skip $skip
b17593289ad0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents: 0
diff changeset
15 #end if
b17593289ad0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents: 0
diff changeset
16 && mv plot.$extension '$output'
0
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
17 ]]>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
18 </command>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
19 <inputs>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
20 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
21 <param name="plot_type" argument="--plot-type" type="select" label="Plot reads or base pairs">
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
22 <option value="reads">Reads</option>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
23 <option value="basepairs">Base pairs</option>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
24 </param>
1
b17593289ad0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents: 0
diff changeset
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
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
26 <expand macro="plot_options" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
27 </inputs>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
28 <outputs>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
29 <expand macro="image_output" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
30 </outputs>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
31 <tests>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
32 <test>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
33 <expand macro="test_input" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
34 <param name="extension" value="png" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
35 <param name="plot_type" value="reads" />
1
b17593289ad0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents: 0
diff changeset
36 <output name="output" file="poretools-yield-plot-out1.png" ftype="png" compare="sim_size" />
0
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
37 </test>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
38 <test>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
39 <expand macro="test_input" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
40 <param name="extension" value="svg" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
41 <param name="plot_type" value="basepairs" />
1
b17593289ad0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
iuc
parents: 0
diff changeset
42 <output name="output" file="poretools-yield-plot-out2.svg" ftype="svg" lines_diff="50" />
0
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
43 </test>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
44 </tests>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
45 <help>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
46 Create a collector’s curve reflecting the sequencing yield over time.
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
47 </help>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
48 <expand macro="citations" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
iuc
parents:
diff changeset
49 </tool>