Mercurial > repos > iuc > purge_dups

annotate macros.xml @ 4:a315c25dc813 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/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
author iuc
date Tue, 12 Oct 2021 19:07:05 +0000
parents
children e9bd16ba5ebd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
1 <macros>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
2 <token name="@TOOL_VERSION@">1.2.5</token>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
3 <token name="@VERSION_SUFFIX@">4</token>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
4 <xml name="xrefs">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
5 <xrefs>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
6 <xref type="bio.tools">purge_dups</xref>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
7 </xrefs>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
8 </xml>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
9 <xml name="trimmers">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
10 <section name="section_hist" title="Histogram plot options" >
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
11 <!--<param name="cutoffs_his" type="data" optional="true" format="txt" label="Read depth cutoffs file" />-->
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
12 <param argument="--ymin" type="integer" optional="true" min="0" label="Specify a minimum for the Y axis"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
13 <param argument="--ymax" type="integer" optional="true" label="Specify a maximum for the Y axis"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
14 <param argument="--xmin" type="integer" optional="true" min="0" label="Specify a minimum for the X axis"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
15 <param argument="--xmax" type="integer" optional="true" label="Specify a maximum for the X axis"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
16 <param argument="--title" type="text" value="Read depth histogram plot" label="Histogram title"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
17 </section>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
18 </xml>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
19 <token name="@HIST_PLOT@"><![CDATA[
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
20 python '$__tool_directory__/hist_plot.py'
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
21 --cutoffs cutoffs.tsv
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
22 #if $function_select.section_hist.ymin
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
23 --ymin $function_select.section_hist.ymin
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
24 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
25 #if $function_select.section_hist.ymax
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
26 --ymax $function_select.section_hist.ymax
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
27 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
28 #if $function_select.section_hist.xmin
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
29 --xmin $function_select.section_hist.xmin
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
30 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
31 #if $function_select.section_hist.xmax
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
32 --xmax $function_select.section_hist.xmax
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
33 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
34 #if $function_select.section_hist.title
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
35 --title '${function_select.section_hist.title}'
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
36 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
37 depth.stat hist.png
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
38 ]]></token>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
39 <token name="@CALCUTS@"><![CDATA[
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
40 calcuts
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
41 #if $function_select.section_calcuts.min_depth:
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
42 -f $function_select.section_calcuts.min_depth
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
43 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
44 #if $function_select.section_calcuts.low_depth:
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
45 -l $function_select.section_calcuts.low_depth
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
46 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
47 #if $function_select.section_calcuts.transition:
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
48 -m $function_select.section_calcuts.transition
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
49 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
50 #if $function_select.section_calcuts.upper_depth:
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
51 -u $function_select.section_calcuts.upper_depth
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
52 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
53 $function_select.section_calcuts.ploidy
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
54 ]]></token>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
55 <xml name="calcuts">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
56 <section name="section_calcuts" title="Calcuts options" expanded="true">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
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"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
58 <param argument="-l" name="low_depth" type="integer" min="0" optional="true" label="Lower bound for read depth" />
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
59 <param argument="-m" name="transition" type="integer" min="0" optional="true" label="Transition between haploid and diploid"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
60 <param argument="-u" name="upper_depth" type="integer" min="0" optional="true" label="Upper bound for read depth" />
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
61 <param name="ploidy" argument="-d" type="select" label="Ploidy" help="Treat as haploid assembly or diploid assembly">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
62 <option value="-d 0" selected="true">Diploid</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
63 <option value="-d 1">Haploid</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
64 </param>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
65 </section>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
66 </xml>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
67 <xml name="output_macro">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
68 <param name="output_options" type="select" multiple="true" display="checkboxes" label="Output files">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
69 <yield />
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
70 <option value="histogram" selected="true">Histogram plot</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
71 <option value="calcuts_cutoff" selected="true">Calcuts cutoff</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
72 <option value="calcuts_log">Calcuts log</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
73 </param>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
74 </xml>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
75 <xml name="requirements">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
76 <requirements>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
77 <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
78 <requirement type="package" version="3.4.2">matplotlib-base</requirement>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
79 </requirements>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
80 </xml>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
81 <xml name="citations">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
82 <citations>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
83 <citation type="doi">10.1093/bioinformatics/btaa025</citation>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
84 </citations>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
85 </xml>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
diff changeset
86 </macros>