Mercurial > repos > iuc > purge_dups

comparison macros.xml @ 4:e17b23c87bf0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
author iuc
date Tue, 12 Oct 2021 19:06:24 +0000
parents
children 1a7b041e3592
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3:bba993929f69 4:e17b23c87bf0
1 <macros>
2 <token name="@TOOL_VERSION@">1.2.5</token>
3 <token name="@VERSION_SUFFIX@">4</token>
4 <xml name="xrefs">
5 <xrefs>
6 <xref type="bio.tools">purge_dups</xref>
7 </xrefs>
8 </xml>
9 <xml name="trimmers">
10 <section name="section_hist" title="Histogram plot options" >
11 <!--<param name="cutoffs_his" type="data" optional="true" format="txt" label="Read depth cutoffs file" />-->
12 <param argument="--ymin" type="integer" optional="true" min="0" label="Specify a minimum for the Y axis"/>
13 <param argument="--ymax" type="integer" optional="true" label="Specify a maximum for the Y axis"/>
14 <param argument="--xmin" type="integer" optional="true" min="0" label="Specify a minimum for the X axis"/>
15 <param argument="--xmax" type="integer" optional="true" label="Specify a maximum for the X axis"/>
16 <param argument="--title" type="text" value="Read depth histogram plot" label="Histogram title"/>
17 </section>
18 </xml>
19 <token name="@HIST_PLOT@"><![CDATA[
20 python '$__tool_directory__/hist_plot.py'
21 --cutoffs cutoffs.tsv
22 #if $function_select.section_hist.ymin
23 --ymin $function_select.section_hist.ymin
24 #end if
25 #if $function_select.section_hist.ymax
26 --ymax $function_select.section_hist.ymax
27 #end if
28 #if $function_select.section_hist.xmin
29 --xmin $function_select.section_hist.xmin
30 #end if
31 #if $function_select.section_hist.xmax
32 --xmax $function_select.section_hist.xmax
33 #end if
34 #if $function_select.section_hist.title
35 --title '${function_select.section_hist.title}'
36 #end if
37 depth.stat hist.png
38 ]]></token>
39 <token name="@CALCUTS@"><![CDATA[
40 calcuts
41 #if $function_select.section_calcuts.min_depth:
42 -f $function_select.section_calcuts.min_depth
43 #end if
44 #if $function_select.section_calcuts.low_depth:
45 -l $function_select.section_calcuts.low_depth
46 #end if
47 #if $function_select.section_calcuts.transition:
48 -m $function_select.section_calcuts.transition
49 #end if
50 #if $function_select.section_calcuts.upper_depth:
51 -u $function_select.section_calcuts.upper_depth
52 #end if
53 $function_select.section_calcuts.ploidy
54 ]]></token>
55 <xml name="calcuts">
56 <section name="section_calcuts" title="Calcuts options" expanded="true">
57 <param argument="-f" name="min_depth" type="float" min="0" max="1" value="0.1" label="Minimum depth count fraction to maximum depth count"/>
58 <param argument="-l" name="low_depth" type="integer" min="0" optional="true" label="Lower bound for read depth" />
59 <param argument="-m" name="transition" type="integer" min="0" optional="true" label="Transition between haploid and diploid"/>
60 <param argument="-u" name="upper_depth" type="integer" min="0" optional="true" label="Upper bound for read depth" />
61 <param name="ploidy" argument="-d" type="select" label="Ploidy" help="Treat as haploid assembly or diploid assembly">
62 <option value="-d 0" selected="true">Diploid</option>
63 <option value="-d 1">Haploid</option>
64 </param>
65 </section>
66 </xml>
67 <xml name="output_macro">
68 <param name="output_options" type="select" multiple="true" display="checkboxes" label="Output files">
69 <yield />
70 <option value="histogram" selected="true">Histogram plot</option>
71 <option value="calcuts_cutoff" selected="true">Calcuts cutoff</option>
72 <option value="calcuts_log">Calcuts log</option>
73 </param>
74 </xml>
75 <xml name="requirements">
76 <requirements>
77 <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement>
78 <requirement type="package" version="3.4.2">matplotlib-base</requirement>
79 </requirements>
80 </xml>
81 <xml name="citations">
82 <citations>
83 <citation type="doi">10.1093/bioinformatics/btaa025</citation>
84 </citations>
85 </xml>
86 </macros>